The raw files were converted to mzXML files with centroiding. The resulting mzXML files were processed by the signal extraction (SE) module of DIA-Umpire to generate pseudo-MSMS spectra. The generated pseudo-MS/MS spectra were searched using X! Tandem, Comet and MSGF+ search engines. The output files from the search engines were further analyzed by PeptideProphet and combined by iProphet. FDR filtering was done with PeptideProphet and ProteinProphet. DIA-Umpire's Quant module was for the quantification analysis. The outputs for all-level quantification (FragSummary, PeptideSummary, ProtSummary) were used in further analysis. The differential abundance analysis was performed by MSstats (v3.10.6) R package. Details for data processing and statistical analysis are available in description.pdf ('Methods' folder).
**Publication : Choi et al. (Under revision) MSstats increases the reproducibility of detecting differentially abundant proteins across tools that process raw mass spectra.
[doi:10.25345/C5RJ0V]
[See
results attachment job
for details]
Keywords: MassIVE.quant reviewed - Platinum
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