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.
