Is there a more-documented protocol on how to use the software? Including examples of what the output should look like.
On Dec 16, 12:08 pm, "Brian Pratt" <[email protected]> wrote: > Something's amiss upstream - without any search results there's nothing to > work with. > > > > -----Original Message----- > From: [email protected] > > [mailto:[email protected]] On Behalf Of Amanda > Sent: Tuesday, December 16, 2008 8:37 AM > To: spctools-discuss > Subject: [spctools-discuss] Re: Reposting- I haven't gotten a response back > yet to my PeptideProphetParser.exe error > > No, I did not see that. My pep.xml looks like this: > > <?xml version="1.0" encoding="UTF-8"?> > <?xml-stylesheet type="text/xsl" href="http://regis- > web.systemsbiology.net/pepXML_std.xsl"?> > <msms_pipeline_analysis date="2008-12-09T10:13:08" xmlns="http://regis- > web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/ > XMLSchema-instance" xsi:schemaLocation="http://regis- > web.systemsbiology.net/pepXML c:\Inetpub\wwwrootpepXML_v110.xsd" > summary_xml="c:/Inetpub/wwwroot/ISB/data/18337.RAW_analysis_test/ > 18337.pep.xml"> > <msms_run_summary base_name="c:/Inetpub/wwwroot/ISB/data/ > 18337.RAW_analysis_test/18337" msManufacturer="Thermo Scientific" > msModel="LTQ FT" msIonization="NSI" msMassAnalyzer="FTMS" > msDetector="unknown" raw_data_type="raw" raw_data=".mzXML"> > <sample_enzyme name="trypsin"> > <specificity cut="KR" no_cut="P" sense="C"/> > </sample_enzyme> > <search_summary base_name="c:/Inetpub/wwwroot/ISB/data/ > 18337.RAW_analysis_test/18337" search_engine="SEQUEST" > precursor_mass_type="average" fragment_mass_type="average" > out_data_type="out" out_data=".tgz" search_id="1"> > <search_database local_path="C:\Inetpub\wwwroot\ISB\data > \Pmarinus_NC_005072.fasta" type="AA"/> > <aminoacid_modification aminoacid="C" massdiff="58.0055" > mass="161.1443" variable="Y" symbol="*"/> > <aminoacid_modification aminoacid="M" massdiff="15.9949" > mass="147.1875" variable="Y" symbol="#"/> > <aminoacid_modification aminoacid="K" massdiff="43.0058" > mass="171.1799" variable="Y" symbol="@"/> > <parameter name="peptide_mass_tol" value="2.000"/> > <parameter name="fragment_ion_tol" value="0.250"/> > <parameter name="ion_series" value=" 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 > 1.0 0.0"/> > <parameter name="max_num_differential_AA_per_mod" value="4"/> > <parameter name="nucleotide_reading_frame" value="0"/> > <parameter name="num_output_lines" value="10"/> > <parameter name="remove_precursor_peak" value="0"/> > <parameter name="ion_cutoff_percentage" value="0.0"/> > <parameter name="match_peak_count" value="0"/> > <parameter name="match_peak_allowed_error" value="1"/> > <parameter name="match_peak_tolerance" value="1.0"/> > <parameter name="protein_mass_filter" value="0 0"/> > <parameter name="sequence_header_filter" value=""/> > </search_summary> > </msms_run_summary> > </msms_pipeline_analysis> > > On Dec 16, 11:12 am, "Brian Pratt" <[email protected]> wrote: > > A "tag" in XML is something like <Hi_I_am_a_tag> > > > So what you're looking for is text beginning "<spectrum_query". > > > -----Original Message----- > > From: [email protected] > > > [mailto:[email protected]] On Behalf Of Amanda > > Sent: Tuesday, December 16, 2008 7:42 AM > > To: spctools-discuss > > Subject: [spctools-discuss] Re: Reposting- I haven't gotten a response > back > > yet to my PeptideProphetParser.exe error > > > Can you explain what a spectrum query tag is? > > > On Dec 15, 10:51 pm, "David Shteynberg" > > <[email protected]> wrote: > > > Hi Amanda, > > > > The error message says: > > > > running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" "c:/ > > > Inetpub/wwwroot/ISB/data/18337.RAW_analysis_test/18337.pep.xml"" > > > file 1: c:/Inetpub/wwwroot/ISB/data/18337.RAW_analysis_test/ > > > 18337.pep.xml > > > processed altogether 0 results > > > > This means there was a problem reading data from your pepXML file. > > > Can you verify that your pepXML fie has spetrum_query tags? > > > > Thanks, > > > -David > > > > On Mon, Dec 15, 2008 at 2:59 PM, Natalie Tasman > > > > <[email protected]> wrote: > > > > Hello Amanda, > > > > > Please try the latest release, 4.1.1 (November) instead of 4.0.2 > (July), > > as > > > > many bugs have been fixed. Perhaps this issue has already been > > addressed. > > > > > Best wishes, > > > > Natalie > > > > > On Mon, Dec 15, 2008 at 2:51 PM, Amanda <[email protected]> > wrote: > > > > >> I'm trying to run Protein prophet but keep running into the same > > > >> error. > > > >> So far, I started with a .RAW file (290MB) and converted it to both > > > >> mzXML (667Mb) and mzML (1GB). I then did a Database search and got > > > >> the > > > >> expected folder with .dta files (2852 files, 1-15KB each). I > > > >> converted these to a .pep.xml file (3KB). The problem comes when I > > > >> try to analyze with Peptide Prophet and Protein Prophet. I get the > > > >> following files: interact.pep.xml, > > > >> interact.pep.shtml,interact.pep.xsl, and interact.pep.xml.tmp.axxxxx. > > > >> I then get the following error messages: > > > >> -------------------------------------- > > > >> Popup message: > > > >> PeptideProphetParser.exe has encountered a problem and needs to > > > >> close. We are sorry for the inconvenience. > > > >> -------------------------------------- > > > >> Error Signature: > > > >> szAppName : PeptideProphetParser.exe szAppVer : 0.0.0.0 > > > >> szModName : PeptideProphetParser.exe szModVer : 0.0.0.0 > > > >> offset : 00019ec0 > > > >> -------------------------------------- > > > >> Error Report Contents: > > > >> C:\DOCUME~1\AMANDA~1\LOCALS~1\Temp > > > >> \WERb712.dir00\PeptideProphetParser.exe.mdmp > > > >> C:\DOCUME~1\AMANDA~1\LOCALS~1\Temp\WERb712.dir00\appcompat.txt > > > >> -------------------------------------- > > > >> Log File/ Output Files: > > > > >> * c:/Inetpub/wwwroot/ISB/data/18337.RAW_analysis_test/ > > > >> interact.pep.shtml [ View ] > > > >> * c:/Inetpub/wwwroot/ISB/data/18337.RAW_analysis_test/ > > > >> interact.prot.shtml (file not found: not created or deleted?) > > > > >> Command 1 [Tue Dec 9 09:33:43 2008] [ Show / Hide ] > > > > >> run_in c:/Inetpub/wwwroot/ISB/data/18337.RAW_analysis_test; > > > >> xinteract -Ninteract.pep.xml -p0.05 -x20 -Op c:/Inetpub/wwwroot/ISB/ > > > >> data/18337.RAW_analysis_test/18337.pep.xml > > > > >> xinteract (TPP v4.0 JETSTREAM rev 2, Build 200807011544 (MinGW)) > > > > >> running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" "c:/ > > > >> Inetpub/wwwroot/ISB/data/18337.RAW_analysis_test/18337.pep.xml"" > > > >> file 1: c:/Inetpub/wwwroot/ISB/data/18337.RAW_analysis_test/ > > > >> 18337.pep.xml > > > >> processed altogether 0 results > > > > >> results written to file c:/Inetpub/wwwroot/ISB/data/ > > > >> 18337.RAW_analysis_test/interact.pep.xml > > > > >> direct your browser to > > > >>http://localhost/ISB/data/18337.RAW_analysis_test/interact.pep.shtml > > > > >> command completed in 1 sec > > > > >> running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" > > > >> MINPROB=0.05 EXTRAITRS=20" > > > >> (SEQUEST) > > > >> MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, > > > >> Ionization: > > > >> UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN > > > > >> command "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" > > > >> MINPROB=0.05 EXTRAITRS=20" failed: Unknown error > > > > >> command "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" > > > >> MINPROB=0.05 EXTRAITRS=20" exited with non-zero exit code: > > > >> -1073741819 > > > >> QUIT - the job is incomplete > > > > >> Command FAILED- Hide quoted text - > > > > - Show quoted text -- Hide quoted text - > > > - Show quoted text -- Hide quoted text - > > - Show quoted text - --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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