Hi,
I'm using PeptideProphet module to process Comet (v 2013010) within the new
version of TPP. Here is the output of comet results in pep.xml format:
</spectrum_query>
<spectrum_query spectrum="elute_F9.17580.17580.2" start_scan="17580"
end_scan="17580" precursor_neutral_mass="2001.8635" assumed_charge="2"
index="3926" retention_time_sec="3984.6">
<search_result>
<search_hit hit_rank="1" peptide="MAVDGGCGDTGDWEGR" peptide_prev_aa="K"
peptide_next_aa="W" protein="sp|Q8TBC4|UBA3_HUMAN" num_tot_proteins="1"
num_matched_ions="1" tot_num_ions="30" calc_neutral_pep_mass="2001.8460"
massdiff="0.0175" num_tol_term="2" num_missed_cleavages="0"
num_matched_peptides="30">
<modification_info modified_peptide="M[147]AVDGGCGDTGDWEGR"
mod_nterm_mass="305.2128">
<mod_aminoacid_mass position="1" mass="147.0354"/>
<mod_aminoacid_mass position="7" mass="160.0306"/>
</modification_info>
<search_score name="xcorr" value="0.088"/>
<search_score name="deltacn" value="0.303"/>
<search_score name="deltacnstar" value="0.000"/>
<search_score name="spscore" value="0.9"/>
<search_score name="sprank" value="2"/>
<search_score name="expect" value="2.15E-130"/>
</search_hit>
Somehow, the peptideprophet only read the expect value, and didn't read
other scores at all.
The veriosn I used was the lasted 4.6.3, and I followed the Sequest
pipeline for comet.
any idea how to fix the problem?
Thank you so much!
sun
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