Deep MALDI-MS spatial omics guided by quantum cascade laser mid-infrared imaging microscopy

Lars Gruber, Stefan Schmidt, Thomas Enzlein, Huong Giang Vo, Tobias Bausbacher, James Lucas Cairns, Yasemin Ucal, Florian Keller, Martina Kerndl, Denis Abu Sammour, Omar Sharif, Gernot Schabbauer, Rüdiger Rudolf, Matthias Eckhardt, Stefania Alexandra Iakab, Laura Bindila and Carsten Hopf ()
Additional contact information
Lars Gruber: Technische Hochschule Mannheim
Stefan Schmidt: Technische Hochschule Mannheim
Thomas Enzlein: Technische Hochschule Mannheim
Huong Giang Vo: Mainz University
Tobias Bausbacher: Technische Hochschule Mannheim
James Lucas Cairns: Technische Hochschule Mannheim
Yasemin Ucal: Technische Hochschule Mannheim
Florian Keller: Technische Hochschule Mannheim
Martina Kerndl: Medical University of Vienna
Denis Abu Sammour: Technische Hochschule Mannheim
Omar Sharif: Medical University of Vienna
Gernot Schabbauer: Medical University of Vienna
Rüdiger Rudolf: Technische Hochschule Mannheim
Matthias Eckhardt: University of Bonn
Stefania Alexandra Iakab: Technische Hochschule Mannheim
Laura Bindila: Mainz University
Carsten Hopf: Technische Hochschule Mannheim

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract In spatial’omics, highly confident molecular identifications are indispensable for the investigation of complex biology and for spatial biomarker discovery. However, current mass spectrometry imaging (MSI)-based spatial ‘omics must compromise between data acquisition speed and biochemical profiling depth. Here, we introduce fast, label-free quantum cascade laser mid-infrared imaging microscopy (QCL-MIR imaging) to guide MSI to high-interest tissue regions as small as kidney glomeruli, cultured multicellular spheroid cores or single motor neurons. Focusing on smaller tissue areas enables extensive spatial lipid identifications by on-tissue tandem-MS employing imaging parallel reaction monitoring-Parallel Accumulation-Serial Fragmentation (iprm-PASEF). QCL-MIR imaging-guided MSI allowed for unequivocal on-tissue elucidation of 157 sulfatides selectively accumulating in kidneys of arylsulfatase A-deficient mice used as ground truth concept and provided chemical rationales for improvements to ion mobility prediction algorithms. Using this workflow, we characterized sclerotic spinal cord lesions in mice with experimental autoimmune encephalomyelitis (EAE), a model of multiple sclerosis, and identified upregulation of inflammation-related ceramide-1-phosphate and ceramide phosphatidylethanolamine as markers of white matter lipid remodeling. Taken together, widely applicable and fast QCL-MIR imaging-based guidance of MSI ensures that more time is available for exploration and validation of new biology by default on-tissue tandem-MS analysis.

Date: 2025
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DOI: 10.1038/s41467-025-59839-3

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