hey matt, thanks for picking this up. i posted the original first lines of the crux file not all the tries to modify them ;-) after fixing the xml structure manually (the originally produced xml file is marked as not well-formed by xmllint), i tried several variations. one of them is posted below:
<?xml version="1.0" encoding="UTF-8"?> <?xml-stylesheet type="text/xsl" href=""?> <msms_pipeline_analysis name="B08-02057" date="Wed Feb 2 14:29:47 2011" xmlns="http://regis-web.systemsbiology.net/pepXML"; xmlns:xsi=" http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation=" http://regis-web.systemsbiology.net/pepXML/usr/local/tpp/schema/pepXML_v110.xsd"; summary_xml="B08-0257.pepXML"> <msms_run_summary base_name="B08-02057" msManufacturer="NA" msModel="NA" msIonization="NA" msAnalyzer="NA" msDectector="NA" raw_data_type="raw" raw_data=".mzXML" > <sample_enzyme name="trypsin"> </sample_enzyme> <search_summary base_name="B08-02057" search_engine="SEQUEST" precursor_mass_type="average" fragment_mass_type="monoisotopic" out_data_type="NA" out_data="NA" search_id="1" > <search_database local_path="/cluster/scratch/malars/databases/AE004092_sp_9606.fasta" type="AA" /> <enzymatic_search_constraint enzyme="trypsin" max_num_internal_cleavages="0" min_number_termini="2"/> <aminoacid_modification aminoacid="C" mass="160.160263" massdiff="57.021464" variable="N" /> it would be great when you could help me adapting the file as i am somehow not pushing the right button. cheers, andreas On Wed, Feb 2, 2011 at 4:25 PM, Matthew Chambers <[email protected]>wrote: > How did it process it as Sequest if the search_engine attribute still says > "Crux"? > > -Matt > > > > On 2/2/2011 5:30 AM, Andreas Quandt wrote: > >> hey jimmy, >> >> thanks for the reply! >> i tried to follow your advice wtih modifying the pepxml produced by crux. >> however it seems i am not pulling the right strings. >> >> when having a crux header like this: >> >> <?xml version="1.0" encoding="UTF-8"?> >> <?xml-stylesheet type="text/xsl" href=""> >> <msms_pipeline_analysis date="Tue Feb 1 23:30:51 2011 >> " xmlns="" xmlns:xsi="" xsi:schemaLocation="" summary_xml=""> >> <msms_run_summary >> base_name="/cluster/scratch/malars/mzxml/plasmaprot/B08-02057.mzXML" >> msManufacturer="NA" msModel="NA" msIonization="NA" msAnalyzer="NA" >> msDectector="NA" >> raw_data_type="NA" raw_data="NA" > >> <sample_enzyme name="trypsin"> >> </sample_enzyme> >> <search_summary >> base_name="/cluster/scratch/malars/mzxml/plasmaprot/B08-02057.mzXML" >> search_engine="Crux" precursor_mass_type="average" >> fragment_mass_type="monoisotopic" >> out_data_type="NA" out_data="NA" search_id="1" > >> <search_database >> >> local_path="/cluster/scratch/malars/databases/AE004092_sp_9606.idx/AE004092_sp_9606-binary-fasta" >> type="AA" /> >> <enzymatic_search_constraint enzyme="trypsin" >> max_num_internal_cleavages="0" min_number_termini="2"/> >> <aminoacid_modification aminoacid="C" mass="160.160263" >> massdiff="57.021464" variable="N" /> >> <parameter name="fragment-mass" value="mono"/> >> >> i tried various modifications of the msms_run_summary and the >> search_summary tags but i always get >> the same error: >> >> read no data >> >> [quandtan@brutus2 crux-output]$ xinteract -dDECOY_ -OAdlIw >> search.mod.pep.xml >> >> running: "/cluster/apps/tpp/4.4.1/bin/PeptideProphetParser >> 'interact.pep.xml' DECOY=DECOY_ ACCMASS >> DECOYPROBS LEAVE PI INSTRWARN" >> using Accurate Mass Bins >> using pI >> Using no error on different instrument types. >> Using Decoy Label "DECOY_". >> Decoy Probabilities will be reported. >> (SEQUEST) (leaving deltacn* entries) >> adding Accurate Mass mixture distr >> adding pI mixture distr >> init with SEQUEST trypsin >> MS Instrument info: Manufacturer: NA, Model: NA, Ionization: NA, Analyzer: >> UNKNOWN, Detector: UNKNOWN >> >> PeptideProphet (TPP v4.4 VUVUZELA rev 1, Build 201102011840 (linux)) >> AKeller@ISB >> read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. >> read in no data >> >> command "/cluster/apps/tpp/4.4.1/bin/PeptideProphetParser >> 'interact.pep.xml' DECOY=DECOY_ ACCMASS >> DECOYPROBS LEAVE PI INSTRWARN" exited with non-zero exit code: 256 >> >> >> can you or probably david point me to what i am doing wrong? >> >> cheers + thanks:-) >> andreas >> > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]<spctools-discuss%[email protected]> > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
