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Related Concept Videos

MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

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Mass spectrometry is a powerful characterization technique that can identify and separate a wide variety of compounds ranging from chemical to biological entities, based on their mass-to-charge ratio (m/z). The instruments that allow this detection, known as mass spectrometers, have three components: an ion source, a mass analyzer, and a detector. These spectrometers differ based on the nature of their ion source and analyzers.Matrix-assisted laser desorption ionization (MALDI) is a commonly...
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An unknown compound can be established by identifying the molecular ion peak in the mass spectrum. The molecular ion peak is often weak or absent due to the predominance of fragmentation in high-energy electron beams. In such cases, a soft-energy electron beam can be used to scan the spectrum to enhance the intensity of the molecular ion peak. Additionally, chemical ionization, field ionization, and desorption ionization spectra are used to obtain a relatively intense molecular ion peak.To...
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Higher molecular weight biomolecules are nonvolatile compounds that may decompose before ionizing or vaporizing during mass analysis with conventional electron impact ionization methods. Accordingly, electrospray ionization (ESI) is the favored method for vaporizing and ionizing biomolecules as it circumvents rapid fragmentation and enables the recording of mass signals for the entire biomolecule.
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Updated: Jan 17, 2026

Whole-body Mass Spectrometry Imaging by Infrared Matrix-assisted Laser Desorption Electrospray Ionization IR-MALDESI
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MSI.EAGLE: An Open-Source GUI for Streamlined Mass Spectrometry Imaging Analysis.

Daniel J Boehmler1,2,3,4, Ashley Woolfork3,4, Ai Wen Tan3,4

  • 1Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA.

Biorxiv : the Preprint Server for Biology
|September 18, 2025
PubMed
Summary
This summary is machine-generated.

Mass Spectrometry Imaging (MSI) analysis is simplified with MSI.EAGLE, an R-Shiny app. This tool empowers non-specialists to analyze complex spatial molecular data effectively.

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Area of Science:

  • Spatial biology
  • Molecular imaging
  • Bioinformatics

Background:

  • Mass Spectrometry Imaging (MSI) enables spatial molecular distribution analysis.
  • Complex MSI data often presents significant analytical challenges.
  • Accessibility for non-specialists remains a barrier in MSI data analysis.

Purpose of the Study:

  • To introduce MSI.EAGLE, an open-source R-Shiny application for MSI data analysis.
  • To enhance the accessibility of advanced MSI analysis tools for a broader scientific audience.
  • To facilitate more effective analysis of spatial molecular distributions.

Main Methods:

  • Development of MSI.EAGLE, an R-Shiny application.
  • Integration of tools from the Cardinal MSI package.
  • Implementation of enhanced phenotyping, segmentation, statistical analysis, and visualization features.

Main Results:

  • MSI.EAGLE provides a user-friendly interface for complex MSI data.
  • The application integrates advanced analytical and visualization tools.
  • It empowers researchers, including non-specialists, in spatial biology.

Conclusions:

  • MSI.EAGLE democratizes MSI data analysis.
  • The application addresses a critical need in spatial biology research.
  • It fosters broader scientific community engagement with MSI techniques.