Hi David, My aim was not to get a meaningful result but to see if peptideprophet could work with the pepxml I'm trying. I used the M2Lite software to transform msf files to pepxml files. The problem is that this option is not yet completely finished and thus I'm looking for the changes requiered so that the pepxml works with peptideprophet. In the example I pasted in the post there were only five peptides because I wanted to see if adding values for "deltacn", "sscan","spscore" and "sprank" would help; with 10 peptides it still doesn't work... I checked the is_rejected="1" in the file created during the begining of peptideprophet and not all the peptides were rejected...
Without the sequest variables and with many peptides I still get the same problem of "read in no data"... Could you tell me what can cause this problem? I don't really know where to look now... Thanks Delphine 2014-06-17 18:56 GMT+02:00 David Shteynberg < [email protected]>: > 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 a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/spctools-discuss/ar-4zUICumc/unsubscribe > . > To unsubscribe from this group and all its topics, 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.
