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

• Published in: Nature communications Vol. 15; no. 1; pp. 9378 - 15
• Main Authors: Dong, Zhen, Jiang, Wenhao, Wu, Chunlong, Chen, Ting, Chen, Jiayi, Ding, Xuan, Zheng, Shu, Piatkevich, Kiryl D., Zhu, Yi, Guo, Tiannan
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 30.10.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 631/1647/2067; 631/45/475; 631/67/2329; 82/58; Colorectal Neoplasms - metabolism; Colorectal Neoplasms - pathology; Formaldehyde; Formaldehyde - chemistry; Humanities and Social Sciences; Humans; Hydrogels; Hydrogels - chemistry; Laser Capture Microdissection - methods; Mass spectrometry; Mass Spectrometry - methods; Mass spectroscopy; multidisciplinary; Organelles; Organelles - metabolism; Paraffin; Paraffin Embedding - methods; Paraffins; Protein folding; Proteomics; Proteomics - methods; Reproducibility of Results; Sample preparation; Science; Science (multidisciplinary); Single-Cell Analysis - methods; Spatial analysis; Tissue Fixation - methods; Tissues; Workflow
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-53683-7

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. Hydrogel-based tissue expansion proteomics represents an emerging spatial proteomics approach. Here, the authors develop the filter-aided expansion proteomics (FAXP) strategy, enabling proteomic analysis of single cells and nuclei in formalin-fixed paraffin-embedded (FFPE) tissue sections.