Hello,
I work in a mass spectrometry data analysis lab. We recently acquired an orbitrap and I would like to use qualscore on these data. I transformed my .raw file to mzxml without any compression, I ran the xtandem identification algorithm and then the peptideProphet algorithm. I use a min prob threshold of 0 in peptide Prophet to keep all the spectra in the analyses. Then I use qualscore on the interact.pep.xml file created : *java -jar -Xmx1500m c:\Inetpub\tpp-bin\qualscore.jar -c 1.0 -p 0.1 -l –a file_interact.pep.xml* The program seems to work fine (see log file joined) but I only get NaN as result for all values. (see joined file) Could you tell me what I did wrong or how to solve the problem? Thanks for your help Delphine -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
C:\Inetpub\wwwroot\ISB\data\300_19_01_130329>java -jar -Xmx1500m
c:\Inetpub\tpp-bin\qualscore.jar -c 1.0 -p 0.1 -l -a
300_19_01_f1p1ns_130402_01_0_interact.pep.xml
QualScore version 1.0_2 Copyright (C) 2006
Institute for Systems Biology, Seattle WA
QualScore is free software and comes with absolutely no warranty.
XML
Loading interact data:
1000 2000 3000 4000 5000 6000 7000 8000 9000 10000 11000 12000 130
00 14000 15000 16000 17000 18000 19000 20000 21000 21238
Interact data file contains 21237 entries.
0 +1 were removed.
Enumerating scans:
processing 300_19_01_F1P1NS_130402_01.mzXML... 500 1000 1500 2000 2500 300
0 3500 4000 4500 5000 5500 6000 6500 7000 7500 8000 8500 9000 9500 10000 10500 1
1000 11500 12000 12500 13000 13500 14000 14500 15000 15500 16000 16500 17000 175
00 18000 18500 19000 19500 20000 20500 21000 21237
Features calculated for: 21237 (477637 ms)
Training set: 837/19001 (good/bad)
Unassigned spectra: 19332
Quality score calculation time: 188 ms
Writing classifier co-efficients to file:
300_19_01_f1p1ns_130402_01_0_interact.pep.xml.all.qual.coef
21237 spectra written to
'300_19_01_f1p1ns_130402_01_0_interact.pep.xml.all.qual'.
Time: 483
300_19_01_F1P1NS_130402_01_0_interact.pep.xml.all.qual.coef
Description: Binary data
