Spatially resolved proteomics is an emerging approach for mapping proteome heterogeneity of biological samples, however, it remains technically challenging due to the complexity of the tissue microsampling techniques and mass spectrometry analysis of nanoscale specimen volumes. Here, we describe a spatially resolved proteomics method based on the combination of tissue expansion with mass spectrometry-based proteomics, which we call Expansion Proteomics (ProteomEx). ProteomEx enables quantitative profiling of the spatial variability of the proteome in mammalian tissues at ~160 µm lateral resolution, equivalent to the tissue volume of 0.61 nL, using manual microsampling without the need for custom or special equipment. We validated and demonstrated the utility of ProteomEx for streamlined large-scale proteomics profiling of biological tissues including brain, liver, and breast cancer. We further applied ProteomEx for identifying proteins associated with Alzheimer’s disease in a mouse model by comparative proteomic analysis of brain subregions.

空间分辨蛋白质组学是一种用于绘制生物样品蛋白质组异质性图谱的新兴方法，但是，由于组织微量采样技术和纳米级标本体积的质谱分析的复杂性，它在技术上仍然具有挑战性。在这里，我们描述了一种基于组织扩展与基于质谱的蛋白质组学相结合的空间分辨蛋白质组学方法，我们称之为扩展蛋白质组学 (ProteomEx)。ProteomEx 能够以约 160 µm 的横向分辨率对哺乳动物组织中蛋白质组的空间变异性进行定量分析，相当于 0.61 nL 的组织体积，使用手动微量采样，无需定制或特殊设备。我们验证并证明了 ProteomEx 在简化生物组织（包括脑癌、肝癌和乳腺癌）的大规模蛋白质组学分析方面的实用性。我们进一步应用 ProteomEx 通过大脑亚区域的比较蛋白质组学分析在小鼠模型中识别与阿尔茨海默氏病相关的蛋白质。