Hi Marco, I am not sure I follow exactly what you've done here. It doesn't appear that you are running ProteinProphet based on the steps you've outlined. I am not surprised the f-val histograms would look different between 2 and 3 since PeptideProphet applies an automatic probability filter of 0.05 % resulting in many wrong id's getting tossed out. To keep these after PeptideProphet use the option MINPROB=0.
-David On Thu, Sep 23, 2010 at 1:37 AM, Marco Schaerfke <[email protected]> wrote: > 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 ZERO > > In 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.xml > Remarkable 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. > > -- 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.
