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.
