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
> >>
> >> --
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> >>
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