Dear TPP experts,
I would like to run PeptideProphet and iProphet.
I use the following command: "xinteract -i -dDECOY -OAdtP -l6 -I1 -I5 -I6
-I7 *xml"
The pepXML contains X!Tandem search results, 22063 in total, only 8 of
which are DECOY matches (reversed sequences, {KR} remain in the same place).
The results were kept with the following expectation cutoffs:
<note type="input" label="output, maximum valid expectation
value">0.01</note>
<note type="input" label="refine, maximum valid expectation
value">0.01</note>
Given that there are only 8 decoys, can PeptideProphet and iProphet succeed
in creating an accurate discriminant function?
Thank you in advance!
Vadim
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