Thanks for sharing the file. I was able to process it using trunk version 5303 using these two commands:
tpp-trunk-5303/bin/InteractParser interact.pep.xml B08-02057_original_crux.pepXML tpp-trunk-5303/bin/PeptideProphetParser interact.pep.xml MINPROB=0 FORCEDISTR The FORCEDISTR option shouldn't normally be used, but if you plot the model returned by this option you can see why the model was auto-rejected by PeptideProphet. In this case it appears that there aren't many positive IDs in the dataset that have scores that are higher than those of the negative model. This holds whether you try it in unsupervised parametric mode, semi-supervised parametric mode, or semi-parametric mode on this dataset. -David On Wed, Feb 2, 2011 at 4:32 PM, Andreas Quandt <[email protected]> wrote: > hey david, > i uploaded 2 files: > 1) the original output file of crux: B08-02057_original_crux.pepXML > 2) the pepxml with the latest modifications/adaptations discussed in this > thread: B08-02057_latest_try_to_adapt.pepXML > the original file is an invalid xml. i already reported this to the > crux-mailing list with with a solution how to fix this and barbara frewen > was already so nice to write a patch for > 1.3.4: http://groups.google.com/group/crux-users/browse_thread/thread/c4df5eeba26d5671 > please let me know when i can be of further help! > cheers, > andreas > > On Thu, Feb 3, 2011 at 1:03 AM, David Shteynberg > <[email protected]> wrote: >> >> 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. >> 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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