Hi Andreas, Would you mind sharing on of your crux pepXML files? You can post it to our ftp site: http://tools.proteomecenter.org/wiki/index.php?title=TPP:Frequently_Asked_Questions#How_do_I_upload_files_to_the_SPC_tools_team.3F
Thanks, -David On Wed, Feb 2, 2011 at 1:08 PM, Andreas Quandt <[email protected]> wrote: > hey david, > thanks for answering! > i used xinteract -dDECOY_ -OAdPlIw B08-02057_mod.pepXML to process the file. > as you suggest using a trunk version: can you refer to a specific revision? > cheers, > andreas > > On Wed, Feb 2, 2011 at 9:57 PM, David Shteynberg > <[email protected]> wrote: >> >> Your best bet is to try the code from trunk SVN. Have you tried it in >> NONPARAM mdoe? >> >> -David >> >> On Wed, Feb 2, 2011 at 12:52 PM, Andreas Quandt >> <[email protected]> wrote: >> > hey jimmy and matt, >> > i tried what jimmy suggested but are stuck again.... :-( >> > i added the 'missing' scores as jimmy suggested: >> > <search_score name="deltacn" value="0.22324939" /> >> > <search_score name="xcorr" value="0.96492940" /> >> > <search_score name="deltacnstar" value="0.000"/> >> > <search_score name="spscore" value="0.0000"/> >> > <search_score name="sprank" value="1"/> >> > and get following output: >> > running: "/cluster/apps/tpp/4.4.1/bin/PeptideProphetParser >> > 'interact.pep.xml' DECOY=DECOY_ ACCMASS DECOYPROBS NONPARAM 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. >> > Using non-parametric distributions >> > (SEQUEST) (leaving deltacn* entries) >> > adding Accurate Mass mixture distr >> > adding pI mixture distr >> > init with SEQUEST trypsin >> > ERROR: Discriminant value computed as nan, for spectrum >> > B08-02057.00210.00210.4. This spectrum will be excluded from the model. >> > ERROR: Discriminant value computed as nan, for spectrum >> > B08-02057.00234.00234.3. This spectrum will be excluded from the model. >> > ERROR: Discriminant value computed as nan, for spectrum >> > B08-02057.00668.00668.2. This spectrum will be excluded from the model. >> > ERROR: Discriminant value computed as nan, for spectrum >> > B08-02057.01888.01888.2. This spectrum will be excluded from the model. >> > ERROR: Discriminant value computed as nan, for spectrum >> > B08-02057.01912.01912.2. This spectrum will be excluded from the model. >> > ERROR: Discriminant value computed as nan, for spectrum >> > B08-02057.01913.01913.2. This spectrum will be excluded from the model. >> > ERROR: Discriminant value computed as nan, for spectrum >> > B08-02057.02423.02423.2. This spectrum will be excluded from the model. >> > ERROR: Discriminant value computed as nan, for spectrum >> > B08-02057.02440.02440.2. This spectrum will be excluded from the model. >> > ERROR: Discriminant value computed as nan, for spectrum >> > B08-02057.02441.02441.2. This spectrum will be excluded from the model. >> > ERROR: Discriminant value computed as nan, for spectrum >> > B08-02057.03150.03150.3. This spectrum will be excluded from the model. >> > ERROR: Discriminant value computed as nan, for spectrum >> > B08-02057.03171.03171.3. This spectrum will be excluded from the model. >> > ERROR: Discriminant value computed as nan, for spectrum >> > B08-02057.04499.04499.3. This spectrum will be excluded from the model. >> > ERROR: Discriminant value computed as nan, for spectrum >> > B08-02057.04599.04599.4. This spectrum will be excluded from the model. >> > ERROR: Discriminant value computed as nan, for spectrum >> > B08-02057.06133.06133.2. This spectrum will be excluded from the model. >> > ERROR: Discriminant value computed as nan, for spectrum >> > B08-02057.06134.06134.2. This spectrum will be excluded from the model. >> > ERROR: Discriminant value computed as nan, for spectrum >> > B08-02057.07676.07676.4. This spectrum will be excluded from the model. >> > 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+, 5 2+, 416 3+, 26 4+, 2 5+, 1 6+, and 0 7+ spectra. >> > Initialising statistical models ... >> > Found 238 Decoys, and 212 Non-Decoys >> > Iterations: .PeptideProphetParser: >> > Validation/InterProphet/InterProphetParser/KDModel.cxx:143: bool >> > KDModel::replaceProb(int, double): Assertion `idx < posprobs_->size()' >> > failed. >> > command "/cluster/apps/tpp/4.4.1/bin/PeptideProphetParser >> > 'interact.pep.xml' >> > DECOY=DECOY_ ACCMASS DECOYPROBS NONPARAM LEAVE PI INSTRWARN" exited with >> > non-zero exit code: 6 >> > QUIT - the job is incomplete >> > the errors are coursed by negative values for the xcorr. hence i >> > 'turned' >> > them into positive values. however this only causes another error: >> > command completed in 1 sec >> > running: "/cluster/apps/tpp/4.4.1/bin/PeptideProphetParser >> > 'interact.pep.xml' DECOY=DECOY_ ACCMASS DECOYPROBS NONPARAM 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. >> > Using non-parametric distributions >> > (SEQUEST) (leaving deltacn* entries) >> > adding Accurate Mass mixture distr >> > adding pI mixture distr >> > init with SEQUEST trypsin >> > command "/cluster/apps/tpp/4.4.1/bin/PeptideProphetParser >> > 'interact.pep.xml' >> > DECOY=DECOY_ ACCMASS DECOYPROBS NONPARAM LEAVE PI INSTRWARN" exited with >> > non-zero exit code: 11 >> > QUIT - the job is incomplete >> > >> > as i do not know what these error codes mean, i am now stuck :-( >> > does one of you guys have a suggestion how to continue? >> > cheers, >> > andreas >> > On Wed, Feb 2, 2011 at 6:49 PM, Andreas Quandt >> > <[email protected]> >> > wrote: >> >> >> >> Hey Jimmy, >> >> >> >> I tried the renaming but of course not the adding of the 'missing' >> >> scoring values. >> >> I report back to you guys as soon as I have tested it :-) >> >> >> >> Cheers, >> >> Andreas >> >> >> >> >> >> >> >> On Feb 2, 2011, at 5:51 PM, Jimmy Eng <[email protected]> wrote: >> >> >> >> > Andreas, >> >> > >> >> > I didn't say it was going to be easy! :) >> >> > >> >> > Here's an example Sequest pep.xml file: >> >> > http://proteomicsresource.washington.edu/dist/sequest.pep.xml >> >> > >> >> > As Matt suggested, the search_score names will need to change >> >> > ("xcorr_score" to "xcorr" and "delta_cn" to "deltacn"). >> >> > Additionally, >> >> > you'll probably want to add "deltacnstar", "spscore", and "sprank" >> >> > score entries. Use 0.0, 0.0, and 1 respectively for the values for >> >> > these additional scores. >> >> > >> >> > - Jimmy >> >> > >> >> > On Wed, Feb 2, 2011 at 8:42 AM, Matthew Chambers >> >> > <[email protected]> wrote: >> >> >> Did you try renaming the score names? I expect that there is a 1:1 >> >> >> relationship between the search engine name and the score names >> >> >> (correct me >> >> >> if I'm wrong TPP folks). If you need a program to do the "replace >> >> >> all" >> >> >> you >> >> >> can try Notepad++ or Gvim. >> >> >> >> >> >> -Matt >> >> >> >> >> >> >> >> >> On 2/2/2011 10:22 AM, Andreas Quandt wrote: >> >> >>> >> >> >>> sure :-) >> >> >>> >> >> >>> originally the spectrum query match looks like >> >> >>> >> >> >>> <spectrum_query spectrum="B08-02057.mzXML.00234.00234.3" >> >> >>> >> >> >>> but after it did not work. i tried the B08-02057.00234.00234.3 >> >> >>> instead: >> >> >>> >> >> >>> >> >> >>> <spectrum_query spectrum="B08-02057.00234.00234.3" start_scan="234" >> >> >>> end_scan="234" >> >> >>> precursor_neutral_mass="1332.6912" assumed_charge="3" index="4"> >> >> >>> <search_result> >> >> >>> <search_hit hit_rank="2" peptide="GAFALTLIGLLLM" >> >> >>> peptide_prev_aa="R" >> >> >>> peptide_next_aa="-" >> >> >>> protein="DECOY_Q8TE58" num_tot_proteins="1" >> >> >>> calc_neutral_pep_mass="1332.7074" massdiff="-0.0162" >> >> >>> num_tol_term="2" num_missed_cleavages="0" is_rejected="0" >> >> >>> protein_descr="\ID=ATS15_HUMAN \MODRES= >> >> >>> \VARIANT=(623|N|S)(770|Q|R)(878|C|G) \NCBITAXID=9606 \DE=A >> >> >>> disintegrin >> >> >>> and >> >> >>> metalloproteinase with >> >> >>> thrombospondin motifs 15 (ADAMTS-15) (ADAM-TS 15) (ADAM-TS15)"> >> >> >>> <search_score name="delta_cn" value="0.00000000" /> >> >> >>> <search_score name="xcorr_score" value="-0.04533549" /> >> >> >>> </search_hit> >> >> >>> </search_result> >> >> >>> </spectrum_query> >> >> >>> <spectrum_query spectrum="B08-02057.00244.00244.5" start_scan="244" >> >> >>> end_scan="244" >> >> >>> precursor_neutral_mass="2591.2581" assumed_charge="5" index="5"> >> >> >>> <search_result> >> >> >>> <search_hit hit_rank="1" peptide="HMLDVLLLFIAVIVALPVLAELGM" >> >> >>> peptide_prev_aa="R" peptide_next_aa="-" >> >> >>> protein="DECOY_P10635" num_tot_proteins="1" >> >> >>> calc_neutral_pep_mass="2591.2922" massdiff="-0.0342" >> >> >>> num_tol_term="2" num_missed_cleavages="0" is_rejected="0" >> >> >>> protein_descr="\ID=CP2D6_HUMAN \MODRES= >> >> >>> >> >> >>> >> >> >>> >> >> >>> \VARIANT=(11|V|M)(26|R|H)(28|R|C)(34|P|S)(42|G|R)(85|A|V)(91|L|M)(94|H|R)(107|T|I)(120|F|I)(155|E|K)(169|G|R)(212|G|E)(231|L|P)(237|A|S)(281|.|)(296|R|C)(297|I|"> >> >> >>> <search_score name="delta_cn" value="0.00000000" /> >> >> >>> <search_score name="xcorr_score" value="0.37809423" /> >> >> >>> </search_hit> >> >> >>> </search_result> >> >> >>> </spectrum_query> >> >> >>> <spectrum_query spectrum="B08-02057.00246.00246.4" start_scan="246" >> >> >>> end_scan="246" >> >> >>> precursor_neutral_mass="2007.0232" assumed_charge="4" index="6"> >> >> >>> <search_result> >> >> >>> >> >> >>> (to the original sequest, the difference is also that the scores >> >> >>> are >> >> >>> named: xcorr and deltacn...) >> >> >>> >> >> >>> --andreas >> >> >>> >> >> >>> On Wed, Feb 2, 2011 at 5:04 PM, Matthew Chambers >> >> >>> <[email protected] >> >> >>> <mailto:[email protected]>> wrote: >> >> >>> >> >> >>> Can you paste a few of the spectrum_query elements? It seems >> >> >>> like >> >> >>> you >> >> >>> got it to process properly >> >> >>> as SEQUEST, so there's something wrong further down. >> >> >>> >> >> >>> -Matt >> >> >> >> >> >> -- >> >> >> 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. >> >> >> >> >> >> >> >> > >> >> > -- >> >> > 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. >> >> > >> > >> > -- >> > 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. >> > >> >> -- >> 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. >> > > -- > 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. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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