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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