Overcoming preservation challenges to enable single-cell proteomics of fixed cell and tissue samples with retained proteome integrity

Abstract

The ability to assay the molecular composition of biological systems with single-cell resolution has revolutionised our understanding of tissue heterogeneity and function. Recent advances in single-cell proteomics (SCP) now enable the unbiased quantification of the proteome to a depth of several thousand proteins across hundreds of cells. Yet the broader adoption beyond specialised groups remains limited due to the need for specific equipment and expertise. A major challenge in making these analyses more broadly available is sample preservation for transporting biological material to SCP-capable facilities. To address this issue and provide practical solutions; we first evaluated various cell preservation methods from monolayer culture samples, then tested our optimised methodology on both cultured cells and, for the first time, preserved animal tissue from an in vivo mouse model. Our findings highlight the feasibility of SCP analyses in preserved tissues, significantly expanding its current applicability. By optimising upstream processing, our approach enables robust single-cell proteome analysis of both cells and tissues, making SCP more accessible to the wider scientific community. Ultimately, this advancement expands the potential applications of SCP, particularly in disciplines where analysing rare or heterogeneous populations is beneficial.