Reanalysis of DIA Data Demonstrates the Capabilities of MS/MS-Free Proteomics to Reveal New Biological Insights in Disease-Related Samples

Data-independent
acquisition (DIA) at the shortened data
acquisition
time is becoming a method of choice for quantitative proteomic applications
requiring high throughput analysis of large cohorts of samples. With
the advent of the combination of high resolution mass spectrometry
with an asymmetric track lossless analyzer, these DIA capabilities
were further extended with the recent demonstration of quantitative
analyses at the speed of up to hundreds of samples per day. In particular,
the proteomic data for the brain samples related to multiple system
atrophy disease were acquired using 7 and 28 min chromatography gradients
(Guzman et al., Nat. Biotech. 2024).
In this work, we applied the recently introduced DirectMS1 method
to reanalysis of these data using only MS1 spectra. Both DirectMS1
and DIA results were matched against long gradient DDA analysis from
the earlier study of the same sample cohort. While the quantitation
efficiency of DirectMS1 was comparable with DIA on the same data sets,
we found an additional five proteins of biological significance relevant
to the analyzed tissue samples. Among the findings, DirectMS1 was
able to detect decreased caspase activity for Vimentin protein in
the multiple system atrophy samples missed by the MS/MS-based quantitation
methods. Our study suggests that DirectMS1 can be an efficient MS1-only
addition to the analysis of DIA data in high-throughput quantitative
proteomic studies.