Data processing was performed as described in the original manuscript, Navarro et al., 2016. 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 (v3.13.5) 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/C5D72D]
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results attachment job
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Keywords: MassIVE.quant reviewed - Platinum
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