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.
