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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