Just to clarify, by "peptides" in the previous message I really meant PSMs (peptide spectrum matches) listed as <spectrum_query.... elements in the pepXML file.
-David On Tue, Jun 17, 2014 at 9:56 AM, David Shteynberg <[email protected]> wrote: > Hi Delphine, > > Perhaps all of the 5 peptides in the file are not of sufficient length > and get set to is_rejected="1" in the pepXML file after > InteractParser, so PeptideProphet cannot use them. Also 5 peptides > are much to few to get a meaningful PeptideProphet result. > > -David > > On Tue, Jun 17, 2014 at 3:38 AM, Delphine <[email protected]> wrote: >> Hello, >> I get this error when I'm using peptideprophet and I would like to >> understand the meaning of the "read in no data", which seems to be the >> beginning of the problem. >> Could someone help me? >> Thanks >> >> Delphine >> >> PS: TPP output: >> >> >> SUCCESS: CORRECTED data file >> C:/Inetpub/wwwroot/ISB/data/test_mslite/TCGA_114C_59-2372-01A-01_24-1548-01A-01_29-1762-01A-01_W_JHUZ_20130903_F1.mzXML >> in msms_run_summary tag ... >> processed altogether 5 results >> INFO: Results written to file: >> c:/Inetpub/wwwroot/ISB/data/test_mslite/interact.pep.xml >> command completed in 1.403e+009 sec >> >> running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml"" >> command completed in 1.403e+009 sec >> >> running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" >> "C:/Inetpub/wwwroot/ISB/data/test_mslite/human.protein.faa"" >> - Searching the tree... >> - Linking duplicate entries... - Printing results... >> >> - Building Commentz-Walter keyword tree...command completed in 1.403e+009 >> sec >> >> running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" >> MINPROB=0.0" >> (SEQUEST) (minprob 0) >> init with SEQUEST trypsin >> MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: >> UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN >> >> PeptideProphet (TPP v4.7 POLAR VORTEX rev 0, Build 201402281256 (MinGW)) >> AKeller@ISB >> read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. >> read in no data >> >> -- >> 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.
