Facile One-Pot Nanoproteomics for Label-Free Proteome Profiling of 50–1000 Mammalian Cells

Recent advances in sample preparation
enable label-free mass spectrometry
(MS)-based proteome profiling of small numbers of mammalian cells.
However, specific devices are often required to downscale sample processing
volume from the standard 50–200 μL to sub-μL for
effective nanoproteomics, which greatly impedes the implementation
of current nanoproteomics methods by the proteomics research community.
Herein, we report a facile one-pot nanoproteomics method termed SOPs-MS
(surfactant-assisted one-pot sample processing at the standard volume coupled with MS) for convenient robust
proteome profiling of 50–1000 mammalian cells. Building upon
our recent development of SOPs-MS for label-free single-cell proteomics
at a low μL volume, we have systematically evaluated its processing
volume at 10–200 μL using 100 human cells. The processing
volume of 50 μL that is in the range of volume for standard
proteomics sample preparation has been selected for easy sample handling
with a benchtop micropipette. SOPs-MS allows for reliable label-free
quantification of ∼1200–2700 protein groups from 50
to 1000 MCF10A cells. When applied to small subpopulations of mouse
colon crypt cells, SOPs-MS has revealed protein signatures between
distinct subpopulation cells with identification of ∼1500–2500
protein groups for each subpopulation. SOPs-MS may pave the way for
routine deep proteome profiling of small numbers of cells and low-input
samples.