Hello,
Some SEQUEST *.out files have uncommon format. In these files there
are multiple lines representing the first hit. The second hit
information starts after several lines of first hit information. For
such OUT files get following XML output (below SEQUEST output
example). The second hit information in XML output is wrong.
Did you come across such OUT files (and see mistake in XML output )?
Please help.
SEQUEST OUT Example: ****************
2009_0813_04.11113.11113.1.out
SEQUEST v.28 (rev. 12), (c) 1998-2007
Molecular Biotechnology, Univ. of Washington, J.Eng/S.Morgan/J.Yates
Licensed to Thermo Fisher Scientific Inc.
08/28/2009, 08:46 PM, 0.0 sec. on EIDOTHEA
(M+H)+ mass = 605.89500 ~ 1.5000 (+1), fragment tol = 2.0000, MONO/
MONO
total inten = 2611.6, lowest Sp = 43.9, # matched peptides = 2351
# amino acids = 28842, # proteins = 75484, F:\Databases
\Human_NCBI_36_3_Rev.fasta, F:\Databases\Human_NCBI_36_3_Rev.fasta.hdr
ion series nABY ABCDVWXYZ: 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0
display top 20/5, ion % = 0.0, CODE = 101040
C=160.03064 M=147.03540 Enzyme:Trypsin(KR) (2)
# Rank/Sp Id# (M+H)+ deltCn XCorr Sp Ions
Reference Peptide
--- -------- -------- -------- ------ ------ ----- ----
--------- -------
1. 1 / 6 10663 607.26819 0.0000 0.2996 43.9 5/ 8 gi|
91206454|ref|NP_001035146.1| +12 -.SSEER.-
22105 gi|149944548|ref|NP_055990.1| neur
31637 gi|91206456|ref|NP_690002.2| hypot
31801 gi|116812577|ref|NP_057103.2| LUC7
34015 gi|169167854|ref|XP_001723047.1| P
34369 gi|169178513|ref|XP_001715551.1| P
39319 gi|157364943|ref|NP_005232.2| ecot
49195 gi|157364945|ref|NP_001098548.2| e
55866 Rev_gi|116008442|ref|NP_055885.3|
56885 gi|63055053|ref|NP_055575.2| TatD
60751 gi|113416552|ref|XP_001128002.1| P
2. 2 / 6 29973 606.32056 0.0226 0.2928 43.9 5/ 8 gi|
156119625|ref|NP_002206.2| +3 -.SSEKR.-
45044 Rev_gi|10863967|ref|NP_066993.1| h
55866 Rev_gi|116008442|ref|NP_055885.3|
55866 Rev_gi|116008442|ref|NP_055885.3|
3. 3 / 6 31801 606.32056 0.0501 0.2846 43.9 5/ 8 gi|
116812577|ref|NP_057103.2| -.SSKER.-
...
**************************************
XML output for above SEQUEST OUT:
**********************
<spectrum_query spectrum="2009_0813_04.11113.11113.1"
start_scan="11113" end_scan="11113" precursor_neutral_mass="604.8877"
assumed_charge="1" index="1123">
<search_result>
<search_hit hit_rank="1" peptide="SSEER" peptide_prev_aa="-"
peptide_next_aa="-" protein="gi|91206454|ref|NP_001035146.1|"
num_tot_proteins="13" num_matched_ions="5" tot_num_ions="8"
calc_neutral_pep_mass="606.2609" massdiff="-1.373190" num_tol_term="2"
num_missed_cleavages="0" is_rejected="0">
<search_score name="xcorr" value="0.300"/>
<search_score name="deltacn" value="0.050"/>
<search_score name="deltacnstar" value="0.000"/>
<search_score name="spscore" value="43.9"/>
<search_score name="sprank" value="6"/>
</search_hit>
<search_hit hit_rank="2" peptide="SSEER" peptide_prev_aa="
is_rejected="0">
<search_score name="xcorr" value="0.000"/>
<search_score name="deltacn" value="0.050"/>
<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>
***********************************************
Thanks,
~Nikhil
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