Subcellular mass spectrometry imaging of lipids and nucleotides using transmission geometry ambient laser desorption and plasma ionisation

Reuben S. E. Young, Ann-Katrin Piper, Luke McAlary, Jayden C. McKinnon, Jeremy S. Lum, Jens Soltwisch, Marcel Niehaus and Shane R. Ellis ()
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Reuben S. E. Young: University of Wollongong
Ann-Katrin Piper: University of Wollongong
Luke McAlary: University of Wollongong
Jayden C. McKinnon: University of Wollongong
Jeremy S. Lum: University of Wollongong
Jens Soltwisch: University of Münster
Marcel Niehaus: Bruker Daltonics GmbH & Co. KG
Shane R. Ellis: University of Wollongong

Nature Communications, 2025, vol. 16, issue 1, 1-13

Abstract: Abstract Demand for mass spectrometry imaging (MSI) technologies offering subcellular resolution for tissues and cell imaging is rapidly increasing. To accomplish this, efficient analyte ionisation is essential, given the small amounts of sample material in each pixel. Herein, we describe an atmospheric pressure transmission-geometry matrix-assisted laser desorption source equipped with plasma ionisation. By utilising a pre-staining method for sample preparation, lipid signal intensities were enhanced by an order of magnitude compared to conventional matrix-only methods, while serendipitously enabling imaging of numerous nucleotides. The system enables detection of up to 200 lipids and nucleotides in tissues at 1 µm-pixel size while informative MSI data is still obtained down to 250 nm pixel size. The use of sub-micron pixels is shown to discern subcellular features through combinations with fluorescence microscopy. This method provides a powerful tool for cellular and sub-cellular imaging of small molecules from tissues and cells for spatial biology applications.

Date: 2025
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DOI: 10.1038/s41467-025-64604-7

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