Overcoming Preservation Challenges to Enable Single-Cell Proteomics of Fixed Cells and Tissue Samples with Retained Proteome Integrity

The ability to assay the molecular
composition of biological
systems
with single-cell resolution has revolutionized 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, broader adoption beyond specialized 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 the transport of 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 optimized methodology on both cultured cells and,
for the first time, preserved animal tissue from an in vivo mouse model. Our findings highlight that the feasibility of SCP
analyses in preserved tissues is more likely to be successful, significantly
expanding its current applicability. By optimizing 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 analyzing rare or heterogeneous
populations is beneficial.