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.