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LipidLocator: an open source Shiny web application for spatial lipidomics.

Prateek Arora1,2, Simon Isfort3,4, Nick Kirschke1,2

  • 1Institute of Anatomy, University of Bern, Bern, 3012, Switzerland.

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|February 11, 2026
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Summary
This summary is machine-generated.

LipidLocator is a new open-source tool that simplifies spatial lipidomics by integrating mass spectrometry imaging data analysis and lipid annotation. This user-friendly application aids in understanding tissue structure and function through lipid distribution studies.

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Area of Science:

  • Biochemistry
  • Analytical Chemistry
  • Bioinformatics

Background:

  • Spatial lipidomics offers insights into tissue structure and function by mapping lipid distribution.
  • Analyzing complex mass spectrometry imaging (MSI) data is challenging due to limitations in high-confidence annotation tools for integrated MSI, MS, and MS/MS pipelines.

Purpose of the Study:

  • To develop an open-source, interactive web application for a unified spatial lipidomics pipeline.
  • To facilitate high-confidence lipid annotation by integrating MSI, MS, and MS/MS data analysis.

Main Methods:

  • Developed LipidLocator, an interactive Shiny web application.
  • Integrated MSI data analysis including normalization, spatial clustering, and differential abundance analysis.
  • Enabled MS and MS/MS-based lipid annotation within a single pipeline.

Main Results:

  • LipidLocator successfully analyzed DESI-MSI and AP-SMALDI data from zebrafish, human renal carcinoma, and mouse brain sections.
  • Demonstrated the ability to segment distinct anatomical structures and tissue sub-regions.
  • Generated high-confidence lipid profiles using integrated MS and MS/MS annotation.

Conclusions:

  • LipidLocator provides an end-to-end, open-source pipeline for spatial lipidomics.
  • It supports various organisms and lipid detection technologies, enhancing lipid imaging studies.
  • The application serves as a valuable, user-friendly resource for lipid metabolism research.