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Analytical challenges in mapping the subcellular metabolome and lipidome
Marta Nobile1, Simone Serrao1, Eleonora Bossi1
1School of Medicine and Surgery, University of Milano-Bicocca, Via Raoul Follereau 3, 20854 Vedano al Lambro, MB, Italy. giuseppe.paglia@unimib.it.
The Analyst
|July 7, 2026
Summary
Organelle-resolved metabolomics and lipidomics analyze cellular chemical composition within specific compartments. This review critically examines mass spectrometry methods for spatial analysis, highlighting limitations and future opportunities.
Area of Science:
- Biochemistry
- Cell Biology
- Analytical Chemistry
Background:
- Mass spectrometry (MS)-based metabolomics and lipidomics are key for cellular chemical analysis.
- Current workflows often assume homogeneous intracellular metabolite/lipid pools, which is insufficient for complex eukaryotic systems.
- Subcellular compartmentalization significantly impacts metabolite/lipid measurement and interpretation.
Purpose of the Study:
- To critically review organelle-resolved metabolomics and lipidomics using a mass spectrometry perspective.
- To evaluate MS-based strategies for analyzing subcellular chemical composition.
- To identify current capabilities, artifacts, and future directions in spatial metabolomics.
Main Methods:
- Comparison of metabolomics and lipidomics studies focusing on subcellular compartments.
- Evaluation of fractionation-based, affinity-based, and spatial MS strategies.
- Review of emerging single-organelle MS techniques like NanoSIMS and DOMS.
Main Results:
- Subcellular compartmentalization is a critical analytical variable, not just a biological feature.
- Existing organelle-resolved MS approaches have limitations in extraction, quantification, and data interpretation.
- Integration of stable isotope tracing enhances spatial metabolomics.
Conclusions:
- Organelle-resolved metabolomics and lipidomics offer powerful insights into cellular chemical heterogeneity.
- Addressing extraction, quantification, and interpretation challenges is crucial for advancing spatial MS.
- Future opportunities lie in integrating advanced MS techniques and stable isotope tracing for comprehensive organelle-level analysis.
