Hi Lars, It appears that the proteins in the pepXML file are all left unmapped after the RefreshParser step. This could be due to RefreshParser not knowing how to deal with your compressed database. You have two options:
The better option is to run RefreshParser on your interact.pep.xml file and give it the uncompressed database. Now you should be able to run ProteinProphet as before. Alternatively you can run ProteinProphet against your file with option UNMAPPED which will allow it to processed UNMAPPED entries. The first option is better because it ensures you have a complete mapping of peptides to proteins in your database. Cheers, -David On Fri, Oct 18, 2013 at 1:56 AM, lars20070 <[email protected]>wrote: > Hi David, > > when running ProteinProphet I encounter a problem similar to the one > posted above: > > WARNING: no data - output file will be empty > My input file interact.pep.xml lists plenty of charge states with > probabilities >0.05. > https://www.dropbox.com/s/iq5v62xtflb5bgt/interact.pep.xml > The prot.xml output is generated but empty. Any suggestions why the spectra > in the input file are ignored? > > Lars > > > ---------------------------------------------------------------------------------------------------------------- > > ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original > Perl by A. Keller (TPP v4.6 OCCUPY rev 3, Build 201307241109 (MinGW)) > (xml input) (no FPKM) (report Protein Length) (using degen pep info) > . . . reading in > c:/Inetpub/wwwroot/ISB/data/comparisonPeakDetection/S/Mascot1/interact.pep.xml. > . . > . . . read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob > 0.05 > WARNING: no data - output file will be empty > > > -- > 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. > For more options, visit https://groups.google.com/groups/opt_out. > -- 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. For more options, visit https://groups.google.com/groups/opt_out.
