Single-Shot 10K Proteome Approach: Over 10,000 Protein Identifications by Data-Independent Acquisition-Based Single-Shot Proteomics with Ion Mobility Spectrometry

The evolution of
mass spectrometry (MS) and analytical techniques
has led to the demand for proteome analysis with high proteome coverage
in single-shot measurements. Focus has been placed on data-independent
acquisition (DIA)-MS and ion mobility spectrometry as techniques for
deep proteome analysis. We aimed to expand the proteome coverage by
single-shot measurements using optimizing high-field asymmetric waveform
ion mobility spectrometry parameters in DIA-MS. With our established
proteome analysis system, more than 10,000 protein groups were identified
from HEK293 cell digests within 120 min of MS measurement time. Additionally,
we applied our approach to the analysis of host proteins in mouse
feces and detected as many as 892 host protein groups (771 upregulated/121
downregulated proteins) in a mouse model of repeated social defeat
stress (R-SDS) used in studying depression. Interestingly, 285 proteins
elevated by R-SDS were related to mental disorders. The fecal host
protein profiling by deep proteome analysis may help us understand
mental illness pathologies noninvasively. Thus, our approach will
be helpful for an in-depth comparison of protein expression levels
for biological and medical research because it enables the analysis
of highly proteome coverage in a single-shot measurement.