Hello Chloe, >From the error log, it seems that the analysis is failing at the PeptideProphet step, and not even making it to Libra. Can you confirm that you get good results with only running PeptideProphet (i.e. no Libra) ? I would suggest that you enable the "MALDI data" option when running the analysis. Cheers, --Luis
On Mon, Jun 23, 2014 at 1:57 PM, Chloe Chien <[email protected]> wrote: > Hi, > > I tried to convert the data generated by a MALDI-TOFTOF with iTRAQ 8plex > labeling into mzXML and went through the pipeline. The database search > using tandem seemed working. However, I couldn't use the generated > tandem.pep.xml file to go through peptideprophet with the Libra function > turned on. (It seemed working okay without Libra) Below was what I got: > > c:\Inetpub\tpp-bin\xinteract (TPP v4.7 POLAR VORTEX rev 1, Build 201405141849 > (MinGW)) > PPM mode in Accurate Mass Model ... > > running: "C:/Inetpub/tpp-bin/InteractParser "Cyto_1-3_Libra_interact.pep.xml" > "Cytosol_OGF1_3_1.tandem.pep.xml" -L"1"" > file 1: Cytosol_OGF1_3_1.tandem.pep.xml > SUCCESS: CORRECTED data file > c:/Inetpub/wwwroot/ISB/data/Cytosol_OGF1_3_1.mzXML in msms_run_summary tag ... > processed altogether 1910 results > INFO: Results written to file: > c:/Inetpub/wwwroot/ISB/data/Cyto_1-3_Libra_interact.pep.xml > command completed in 1 sec > > running: "C:/Inetpub/tpp-bin/DatabaseParser "Cyto_1-3_Libra_interact.pep.xml"" > command completed in 0 sec > > running: "C:/Inetpub/tpp-bin/RefreshParser "Cyto_1-3_Libra_interact.pep.xml" > "c:/Inetpub/wwwroot/ISB/data/parameters/Uniprot_sprot_human_mouse_2014.fasta"" > - Searching the tree... > - Linking duplicate entries... - Printing results... > > - Building Commentz-Walter keyword tree...command completed in 5 sec > > running: "C:/Inetpub/tpp-bin/PeptideProphetParser > "Cyto_1-3_Libra_interact.pep.xml" MINPROB=0.05 PPM MALDI" > using PPM mass difference > maldi mode > (X! Tandem (k-score)) > init with X! Tandem (k-score) trypsin > MS Instrument info: Manufacturer: AB SCIEX, Model: TOF/TOF 5800, Ionization: > matrix-assisted laser desorption ionization, Analyzer: time-of-flight, > Detector: microchannel plate detector > > PeptideProphet (TPP v4.7 POLAR VORTEX rev 1, Build 201405141849 (MinGW)) > AKeller@ISB > read in 1910 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. > > command "C:/Inetpub/tpp-bin/PeptideProphetParser > "Cyto_1-3_Libra_interact.pep.xml" MINPROB=0.05 PPM MALDI" failed: Unknown > error > > command "C:/Inetpub/tpp-bin/PeptideProphetParser > "Cyto_1-3_Libra_interact.pep.xml" MINPROB=0.05 PPM MALDI" exited with > non-zero exit code: 255 > QUIT - the job is incomplete > > command "c:\Inetpub\tpp-bin\xinteract -NCyto_1-3_Libra_interact.pep.xml > -p0.05 -l1 -PPM -Om -Lcondition.xml-1 Cytosol_OGF1_3_1.tandem.pep.xml" > failed: Unknown error > > *Command FAILED* > RETURN CODE:65280 > > Is there anything I should modify on the settings? > > Thanks, > > Chloe > > -- > 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/d/optout. > -- 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/d/optout.
