hey david, jimmy and matt, many thanks to all of you for looking into it and offering your help
@david: i am very glad to hear that you were able to process the file. as this was my first try with crux i am also not surprised that the model was awful. also as you suggested, i will try to install the r5303 to see if i can process the files on my own and getting better models in future ;-) again, many thanks to all of you! cheers, andreas On Thu, Feb 3, 2011 at 7:16 PM, David Shteynberg < [email protected]> wrote: > 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]<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]<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. 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