Team: Maarten Bijlsma and Guus Smit

Recognizing that proteins are the primary effectors of cellular function, SCAPE (Single Cell Adore Proteomics Exploration Unit) seeks to overcome the limitations of traditional bulk proteomics by enabling the analysis of protein expression and modifications at the single-cell level.

This approach provides unprecedented insights into cellular heterogeneity, tissue architecture, and disease mechanisms, which are often masked in bulk analyses.

Recent technological advances in sample preparation, chromatography, mass spectrometry, and data processing have made single-cell proteomics increasingly feasible. SCAPE will leverage these developments by establishing a specialized unit within the Amsterdam UMC Proteomics Core Resource. The unit will be equipped with state-of-the-art instruments, including the cellenONE for precise single-cell handling, the Evosep liquid chromatography system for high-throughput peptide separation, and the timsTOF Ultra mass spectrometer for ultra-sensitive protein detection. Additionally, advanced computational infrastructure will be implemented to manage and analyze the complex datasets generated.

A key innovation of SCAPE is its integration of spatial information, allowing researchers to correlate proteomic data with tissue context. Techniques such as Deep Visual Proteomics (DVP) will enable the identification and isolation of specific cell types from tissue sections, further enhancing the biological relevance of the findings. The project will also benefit from collaborations with experts in cell-cell computation, spatial omics, and data visualization, ensuring comprehensive and cutting-edge analysis.

Ultimately, SCAPE aims to drive breakthroughs in cancer and neuroscience research by revealing the functional diversity of individual cells, identifying novel biomarkers and therapeutic targets, and fostering a collaborative, data-driven research environment within the Adore ecosystem.