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]>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
>
>
>
> On 2/2/2011 9:56 AM, Andreas Quandt wrote:
>
>> hey matt,
>>
>> thanks for picking this up.
>> i posted the original first lines of the crux file not all the tries to
>> modify them ;-)
>> after fixing the xml structure manually (the originally produced xml file
>> is marked as not
>> well-formed by xmllint), i tried several variations. one of them is posted
>> below:
>>
>> <?xml version="1.0" encoding="UTF-8"?>
>> <?xml-stylesheet type="text/xsl" href=""?>
>> <msms_pipeline_analysis name="B08-02057" date="Wed Feb 2 14:29:47 2011"
>> xmlns="http://regis-web.systemsbiology.net/pepXML";
>> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
>> xsi:schemaLocation="http://regis-web.systemsbiology.net/pepXML
>> /usr/local/tpp/schema/pepXML_v110.xsd" summary_xml="B08-0257.pepXML">
>> <msms_run_summary base_name="B08-02057" msManufacturer="NA" msModel="NA"
>> msIonization="NA"
>> msAnalyzer="NA" msDectector="NA" raw_data_type="raw" raw_data=".mzXML" >
>> <sample_enzyme name="trypsin">
>> </sample_enzyme>
>> <search_summary base_name="B08-02057" search_engine="SEQUEST"
>> precursor_mass_type="average"
>> fragment_mass_type="monoisotopic" out_data_type="NA" out_data="NA"
>> search_id="1" >
>> <search_database
>> local_path="/cluster/scratch/malars/databases/AE004092_sp_9606.fasta"
>> type="AA" />
>> <enzymatic_search_constraint enzyme="trypsin"
>> max_num_internal_cleavages="0" min_number_termini="2"/>
>> <aminoacid_modification aminoacid="C" mass="160.160263"
>> massdiff="57.021464" variable="N" />
>>
>> it would be great when you could help me adapting the file as i am somehow
>> not pushing the right button.
>>
>> cheers,
>> andreas
>>
>
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