Spatial proteomics of single cells and organelles on tissue slides using filter-aided expansion proteomics

Zhen Dong, Wenhao Jiang, Chunlong Wu, Ting Chen, Jiayi Chen, Xuan Ding, Shu Zheng, Kiryl D. Piatkevich (), Yi Zhu () and Tiannan Guo ()
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Zhen Dong: Westlake University
Wenhao Jiang: Westlake University
Chunlong Wu: Westlake University
Ting Chen: Zhejiang University
Jiayi Chen: Westlake University
Xuan Ding: Westlake University
Shu Zheng: Zhejiang University
Kiryl D. Piatkevich: Westlake Laboratory of Life Sciences and Biomedicine
Yi Zhu: Westlake University
Tiannan Guo: Westlake University

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: Abstract Hydrogel-based tissue expansion combined with mass spectrometry (MS) offers an emerging spatial proteomics approach. Here, we present a filter-aided expansion proteomics (FAXP) strategy for spatial proteomics analysis of archived formalin-fixed paraffin-embedded (FFPE) specimens. Compared to our previous ProteomEx method, FAXP employed a customized tip device to enhance both the stability and throughput of sample preparation, thus guaranteeing the reproducibility and robustness of the workflow. FAXP achieved a 14.5-fold increase in volumetric resolution. It generated over 8 times higher peptide yield and a 255% rise in protein identifications while reducing sample preparation time by 50%. We also demonstrated the applicability of FAXP using human colorectal FFPE tissue samples. Furthermore, for the first time, we achieved bona fide single-subcellular proteomics under image guidance by integrating FAXP with laser capture microdissection.

Date: 2024
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DOI: 10.1038/s41467-024-53683-7

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