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 <matt.chamber...@gmail.com> 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 >> <matt.chamber...@gmail.com >> <mailto:matt.chamber...@gmail.com>> 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 spctools-discuss@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > 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 spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
