Cell Storage Conditions Impact Single-Cell Proteomic Landscapes

Single cell transcriptomics (SCT) has revolutionized
our understanding
of cellular heterogeneity, yet the emergence of single cell proteomics
(SCP) promises a more functional view of cellular dynamics. A challenge
is that not all mass spectrometry facilities can perform SCP, and
not all laboratories have access to cell sorting equipment required
for SCP, which together motivate an interest in sending bulk cell
samples through the mail for sorting and SCP analysis. Shipping requires
cell storage, which has an unknown effect on SCP results. This study
investigates the impact of cell storage conditions on the proteomic
landscape at the single cell level, utilizing Data-Independent Acquisition
(DIA) coupled with Parallel Accumulation Serial Fragmentation (diaPASEF).
Three storage conditions were compared in 293T cells: (1) 37 °C
(control), (2) 4 °C overnight, and (3) −196 °C storage
followed by liquid nitrogen preservation. Both cold and frozen storage
induced significant alterations in the cell diameter, elongation,
and proteome composition. By elucidating how cell storage conditions
alter cellular morphology and proteome profiles, this study contributes
foundational technical information about SCP sample preparation and
data quality.