Hi All, I was trying to use PeptideProphet in TPP software package (TPP v4.3 JETSTREAM rev 1, Build 200909091257 (MinGW)) to calculate PSM probabilities for my Mascot search result. I was able to convert Mascot.dat file to pepXML format. But I am encountering some problems with PeptideProphet and ProteinProphet.
In my Mascot result, I was able to identify 2353 peptides and 538 proteins (E.coli cell lysates) at the significance threshold of 0.05. But after I ran Xinteract in TPP, the number of peptide identifications with probability higher than 0.1 was only 428. The total PSM number was 2463. So I took a close look at the result, some probability calculation doesn't make sense to me. For example, in the mascot result, one PSM had an ion score of 197.22, but the converted probability was only 0.0013. And this is not the only case. In total there are 352 peptide identification with ion score higher than 80 but probability lower than 0.1. Then I plotted Mascot Ion score against the calculated PeptideProphet probability. There seems to be little correlation. I uploaded the figure if you are interested (IonScoreVSProbability.jpg). I suspected there might be some problems with the conversion or certain parameters I forgot to choose or optimize. I also uploaded the pepXML file, so you can give a try (F057073.pep.xml). Is there anyone encountering similar problem as me? Any help will be appreciated. Below is the information I got when ran Xinteract: un_in c:/Inetpub/wwwroot/ISB/data; c:\Inetpub\tpp-bin\xinteract - Ninteract.pep.xml -p0 -l5 -Op c:/Inetpub/wwwroot/ISB/data/ F057073.pep.xml c:\Inetpub\tpp-bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build 200909091257 (MinGW)) running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" "c:/ Inetpub/wwwroot/ISB/data/F057073.pep.xml" -L"5"" file 1: c:/Inetpub/wwwroot/ISB/data/F057073.pep.xml processed altogether 3171 results results written to file c:/Inetpub/wwwroot/ISB/data/interact.pep.xml direct your browser to http://localhost/ISB/data/interact.pep.shtml command completed in 2 sec running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" MINPROB=0" (MASCOT) (minprob 0) results for charge 1: 17 id tot and 0 adj scores results for charge 2: 2098 id tot and 431 adj scores ...skipping 45 lines of output... . . . read in 0 1+, 454 2+, 62 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 INFO: mu=1.46739e-005, db_size=5594906 protein probabilities written to file c:/Inetpub/wwwroot/ISB/data/ interact.prot.xml direct your browser to http://localhost/ISB/data/interact.prot.shtml command completed in 2 sec running: "C:/Inetpub/tpp-bin/ProtProphModels.pl -i interact.prot.xml" Analyzing interact.prot.xml ... command completed in 0 sec C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" "c:/Inetpub/ wwwroot/ISB/data/F057073.pep.xml" -L"5" 2 sec C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" MINPROB=0 3 sec C:/Inetpub/tpp-bin/ProphetModels.pl -i interact.pep.xml 1 sec C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml" C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" "c:/Inetpub/ wwwroot/ISB/data/dbase/EcoliK12_1.fasta" 3 sec c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ ISB/data/interact.pep.xml 1 sec C:/Inetpub/tpp-bin/ProteinProphet "interact.pep.xml" "interact.prot.xml" XML 2 sec C:/Inetpub/tpp-bin/ProtProphModels.pl -i interact.prot.xml 0 sec job completed in 12 sec Command Successful Ming Dec. 15, 2009 -- 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.
