Hi,I use the TPP 4.4 command line tools in combination with Mascot 2.3. I am not able to understand the output of the ProteinProphet (please see attached file).
Procedure: 1. Mascot2XML.exe Mascotdatfile -Dfastafile -notgz -shortid 2. InteractParser.exe interact.xml pepxmlfile -X1 -L5 3. PeptideProphetParser.exe interact.xml INSTWARN ZEROIn the attached file you can see a histogram of the ionscores extracted from the interact.xml (top) for the 2+ charged ions.
The second plot is a histogram of the fvals also from the interact.xmlRemarkable is the peak (fval ~ -1.5 with a frequency about 1800), I would expect this with respect to the ionscore plot. Therefore I have implemented my own fval calculation program with this formula (-3 +0.1*(ionscore - identityscore + AverageidentityScore) ... this could be wrong, but I found no better documentation. The result is show in the last histogram. Interestingly there is no peak at -1.5, but the rest of the histogram is similar.
I am unable to understand the TPP behavior, may be a bug ? Cheers Marco -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
TPP4.4-Mascot.pdf
Description: Adobe PDF document
