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bioRxiv · 10.1101/2023.11.29.569242

Filter-aided expansion proteomics

Dong, Z.·Zhu, Y.·Zhang, F.·Wu, C.·Chen, T.·Jiang, W.·Xiao, Q.·Zheng, S.·Piatkevich, K. D.·Guo, T.
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Abstract

Integration of hydrogel-based tissue expansion and mass spectrometry-based proteomics enables high spatial resolution analysis of global protein expression in tissues. Here, we introduce a filter-aided tissue expansion proteomics (FAXP) method with optimized hydrogel preparation and treatment steps for spatial proteomics analysis of formalin-fixed paraffin-embedded (FFPE) specimens. Compared with our original ProteomEx method, FAXP, partially automated with robotics, exhibited 14.5-fold higher volumetric resolution, increased peptide yield leading to 250% more protein identifications, and 50% time consumption for sample preparation. We demonstrated its application in clinical colorectal tissue samples. We further integrated it with laser capture microdissection for proteomic analysis of subcellular organelles.

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Dong, Z., Zhu, Y., Zhang, F., Wu, C., Chen, T., Jiang, W., Xiao, Q., Zheng, S., Piatkevich, K. D., Guo, T.. 2023-11-29. Filter-aided expansion proteomics. https://doi.org/10.1101/2023.11.29.569242

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