Multiplexed Enzyme Activity Microscopy by Semi-quantitative, Ratiometric Enzyme Activity MALDI Mass Spectrometry Imaging

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Abstract Enzymes are often tightly regulated and exist in inactive forms. Therefore, rather than mere presence, it is the enzyme’s activity that catalyzes cellular and tissue functions. However, multiplex activity mapping of enzymes in situ is particularly challenging. To address this, we introduce multiplexed enzyme activity MALDI–MSI (MEA–MSI), a ratiometric, semi-quantitative method that allows multiplex in situ visualization of enzyme activities in zinc-fixed tissue sections. To accomplish this, a library of 31 MEA–MSI substrates targeting proteases, kinases, histone acetyltransferases, and glycosyltransferases was synthesized. Each substrate is designed so that the masses of these substrates and their enzymatic products are distinct, enabling their simultaneous pixel-wise detection within tissue sections. A ratiometric calculation procedure was used to estimate the relative enzyme activity and compensate for tissue-dependent ionization bias, which is a general problem in MALDI–MSI. MEA–MSI was applied to healthy mouse liver, a murine hepatocellular carcinoma (HCC) model, and an incomplete microwave-ablated (iMWA) rabbit VX2 liver tumor model. The resulting activity maps revealed distinct regional enzyme activity patterns across tumor and normal tissues. Correlation and network analyses showed related enzyme activities and related groups, while unsupervised clustering and Uniform Manifold Approximation and Projection (UMAP) analysis reproduced histological patterns. Because MEA–MSI relies on enzymatic amplification, it is not restricted to the detection of highly abundant enzymes and enables multiplexed, spatially resolved readouts of enzyme activity in situ, providing a framework for comparative spatial enzymology.

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