Mass spectrometry imaging (MSI) enables label-free spatial mapping of hundreds of biomolecules in tissue sections. This capability provides valuable information on tissue heterogeneity that is difficult to obtain using population-averaged assays. Despite substantial developments in both instrumentation and methodology, MSI of tissue samples at single-cell resolution remains challenging. Herein, we describe a protocol for robust imaging of tissue sections with a high (better than 10-μm) spatial resolution using nanospray desorption electrospray ionization (nano-DESI) mass spectrometry, an ambient ionization technique that does not require sample pretreatment before analysis. In this protocol, mouse uterine tissue is used as a model system to illustrate both the workflow and data obtained in these experiments. We provide a detailed description of the nano-DESI MSI platform, fabrication of the nano-DESI and shear force probes, shear force microscopy experiments, spectral acquisition, and data processing. A properly trained researcher (e.g., technician, graduate student, or postdoc) can complete all the steps from probe fabrication to data acquisition and processing within a single day. We also describe a new strategy for acquiring both positive- and negative-mode imaging data in the same experiment. This is achieved by alternating between positive and negative data acquisition modes during consecutive line scans. Using our imaging approach, hundreds of high-quality ion images were obtained from a single uterine section. This protocol enables sensitive and quantitative imaging of lipids and metabolites in heterogeneous tissue sections with high spatial resolution, which is critical to understanding biochemical processes occurring in biological tissues.
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The data presented in this study are available from the corresponding author upon reasonable request.
The LabVIEW and MSI QuickView programs are available from the corresponding author upon reasonable request.
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This work was supported by the National Institutes of Health (NIH) Common Fund, through the Office of Strategic Coordination/Office of the NIH Director under award UG3HL145593 (HuBMAP Program, J.L. and K.E.B.-J.), the NIH Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD, grant R21 HD084788 to K.E.B.-J.), and NIH grants (DA006668 and HD068524 to S.K.D.).
The authors declare no competing interests.
Peer review information Nature Protocols thanks Pierre Chaurand and Livia Schiavinato Eberlin for their contribution to the peer review of this work.
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Key references using this protocol
Nguyen, S. N. et al. J. Am. Soc. Mass Spectrom. 29, 316–322 (2018): https://doi.org/10.1007/s13361-017-1750-8
Yin, R. et al. Anal. Chem. 90, 6548–6555 (2018): https://doi.org/10.1021/acs.analchem.8b00161
Nguyen, S. N., Liyu, A. V., Chu, R. K., Anderton, C. R. & Laskin, J. Anal. Chem. 89, 1131–1137 (2016): https://doi.org/10.1021/acs.analchem.6b03293
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Yin, R., Burnum-Johnson, K.E., Sun, X. et al. High spatial resolution imaging of biological tissues using nanospray desorption electrospray ionization mass spectrometry. Nat Protoc 14, 3445–3470 (2019) doi:10.1038/s41596-019-0237-4