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]<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]<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]<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.
