Fast and sensitive spatial proteomics using laser capture microdissection and a protein immobilization-based...

Biological tissues are spatially organized and contain diverse cell populations with distinct local functions. Spatial proteomics aims to measure protein expression in its native tissue context, but the spatial resolution of liquid chromatography tandem mass spectrometry (LC-MS/MS)-based workflows is often limited by sample loss during preparation, which reduces sensitivity for microscale inputs.

In this study, we developed a protein immobilization-based capillary microreactor (PICR) and combined it with laser capture microdissection (LCM) to enable high-resolution spatial proteome profiling. Notably, the PICR-based sample processing requires less than 1 h. Using the LCM-PICR workflow, we identified more than 1700 proteins from tumor tissue microdissected regions with an estimated volume of 1.0 × 10^-5 mm³ (8 μm thickness; ∼20 μm radius). Spatial analysis revealed 56 proteins with significant abundance differences between central and peripheral regions. In addition, 20 proteins showed monotonic abundance trends that followed the spatial ordering of the sampled regions. Several spatially associated proteins, including NPM1, IMPDH2, CA9, and PDK3, were consistent with functional features of tumor periphery and hypoxic tumor cores.

The LCM-PICR workflow provides a rapid and sensitive sample processing strategy for LC-MS/MS-based spatial proteomics from micrometer-scale tissue regions. This approach supports detection of spatially structured protein variation within tumors and offers a practical tool for studying intratumoral heterogeneity and spatially resolved disease biology.