Hello Delphine, I believe your pepXML file specifies search_engine="SEQUEST" and only lists the xcorr aunder the search_score tag . PeptideProphet will expect each spectrum_query/search_hit to have the following scores:
<search_score name="xcorr" value="2.696"/> <search_score name="deltacn" value="0.408"/> <search_score name="deltacnstar" value="0"/> <search_score name="spscore" value="400.7"/> <search_score name="sprank" value="2"/> PeptideProphet only utilizes search_hits of hit_rank="1" -David On Wed, Jun 18, 2014 at 7:00 AM, Eric Deutsch <[email protected]> wrote: > There are many things that could be wrong. It would probably be most > efficient if you would make available to us some of these files, perhaps the > originals and ones that you have attempted to fix. We could probably come up > with an example of a file that can be processing by PeptideProphet and then > you could ask the M2Lite developers to fix the exported pepXML to be > complete. > > > > Regards, > > Eric > > > > > > From: [email protected] > [mailto:[email protected]] On Behalf Of delphine wood > Sent: Wednesday, June 18, 2014 1:30 AM > To: [email protected] > Subject: Re: [spctools-discuss] peptide prophet "read in no data" > > > > 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. > > -- > 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. 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