Is there a way to retain quantified peptides for the protein quant with Libra? I understand that Libra discards peptides without all channels...what about in instances where the you expect there to be little or no intensity? I have data from pulldowns where we don't expect to see much of the protein in the presence of a competitive inhibitor, so in this case it would be of use to retain such quants where the intensity is zero in the presence of inhibitor but several thousands in the pulldown channel...Is there a way to toggle on/off the peptides that are used for the protein quant in Libra? I'm thinking along the lines like in Xpress where you can toggle whether or not a peptide is used for the protein quant. Is there also a way to modify the number of standard deviations that are used to discard a peptide from being used in the protein quant?
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