Hi all, I ran the analysis by Mascot followed with PeptideProphet and ProteinProphet post-processing. In Mascot method, I defined the species to be Rat only and the Mascot results only showed me the Rat proteins. However, the ProteinProphet results gave me the results from all species. So is there anyway that the ProteinProphet only show the species I am interested in?
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