School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China.
Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China.
Nat Commun. 2024 Oct 30;15(1):9378. 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.
水凝胶组织扩张联合质谱（MS）提供了一种新兴的空间蛋白质组学方法。在这里，我们提出了一种过滤辅助扩张蛋白质组学（FAXP）策略，用于分析存档的福尔马林固定石蜡包埋（FFPE）标本的空间蛋白质组学。与我们之前的 ProteomEx 方法相比，FAXP 采用了定制的尖端设备，提高了样品制备的稳定性和通量，从而保证了工作流程的可重复性和稳健性。FAXP 实现了 14.5 倍的体积分辨率提高。它产生了超过 8 倍的肽产量和 255%的蛋白质鉴定增加，同时将样品制备时间缩短了 50%。我们还使用人结直肠 FFPE 组织样本证明了 FAXP 的适用性。此外，我们首次通过将 FAXP 与激光捕获显微解剖相结合，在图像引导下实现了真正的单细胞蛋白质组学。
