Hello,
I generated *.pep.xml files from SEQUEST out files using OUT2XML.exe.
I generrate output for 1st two hits. However, for some search hits, I
see the probelm as explained below.
For one sepctrum it generated following line for hit 2:
<search_hit hit_rank="2" peptide="DNIQGITKPAIRR" peptide_prev_aa="
is_rejected="0">
Because of such incorrect lines the XML reader cannot read the files
correctly (through Java or C#). Do you know how to fix such error
lines?
Thanks,
~Nikhil.
Complete output as shown below:
*************************
<spectrum_query spectrum="2009_0813_04.10119.10119.2"
start_scan="10119" end_scan="10119" precursor_neutral_mass="1481.4557"
assumed_charge="2" index="139">
<search_result>
<search_hit hit_rank="1" peptide="DNIQGITKPAIRR"
peptide_prev_aa="-" peptide_next_aa="-" protein="gi|28173560|ref|
NP_778224.1|" num_tot_proteins="14" num_matched_ions="14"
tot_num_ions="24" calc_neutral_pep_mass="1480.8475"
massdiff="+0.608260" num_tol_term="2" num_missed_cleavages="0"
is_rejected="0">
<search_score name="xcorr" value="0.937"/>
<search_score name="deltacn" value="0.079"/>
<search_score name="deltacnstar" value="0.000"/>
<search_score name="spscore" value="249.4"/>
<search_score name="sprank" value="19"/>
</search_hit>
<search_hit hit_rank="2" peptide="DNIQGITKPAIRR"
peptide_prev_aa=" is_rejected="0">
<search_score name="xcorr" value="0.000"/>
<search_score name="deltacn" value="0.079"/>
<search_score name="deltacnstar" value="0.000"/>
<search_score name="spscore" value="0.0"/>
<search_score name="sprank" value="0"/>
</search_hit>
</search_result>
</spectrum_query>
*****************************************************
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