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 On Wed, Feb 2, 2011 at 2:35 AM, Jimmy Eng <[email protected]> wrote: > Andreas, > > There's definitely no support for Crux in TPP 4.4.1 if that's what you > tried. The semi good news is that David does have code in the Sashimi > SourceForge repository to start supporting Crux so maybe it'll work in > the next full TPP release. You might be able to push analysis through > by editing your Crux pep.xml file and making it look like a Sequest > pep.xml file for the time being. > > On Tue, Feb 1, 2011 at 3:18 PM, Andreas Quandt <[email protected]> > wrote: > > dear list, > > i tried processing some pep.xml produced by crux with the tpp. > > however i get always the same error message (i tried xinteract and the > > peptideprophetparser both with the Pd option): > > error: engine Crux not recognized > > is the any possible chance to process these results with the tpp? > > cheers, > > 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]<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.
