X!Tandem Output vs PepXML

[EddieMu]

Hi,

I have recently converted an X!Tandem output file to PepXML format
using Tandem2XML utility. The X!Tandem output file was generated from
an MGF file. After the conversion, I compared the contents of the X!
Tandem output and PepXML files to try to determine which attributes in
the PepXML file represent related attributes in the X!Tandem output
file. It seems that not all attributes that we deem important (for a
project we are doing) in the X!Tandem output are represented in the
PepXML file.

The crucial question is: What attributes in the X!Tandem output file
are NOT represented in the PepXML file? One of the most important
attribute to us that we didn't seem to see in the PepXML file was the
"start" attribute that is used to indicate where the peptide sequence
begins in the protein. Below are tables that show what we have in the
X!Tandem file and the perceived equivalent in the PepXML file. Kindly
help me determine if my comparison is correct and what I may be
missing (Not Found) in PepXML format that actually exists.

Also, how do the MASCOT output files compare to PepXML files? Does
the same issue of “missing” attributes also exist?

Thanks in advance.

Protein Info
X!Tandem Output Field PepXML Field Comments
./protein[1]/label ./spectrum_query/search_result/search_hit/protein

./protein[1]/id ./spectrum_query/start_scan

./protein[1]/uid Not found
./protein[1]/sumI Not found
./protein[1]/expect Not found

Peptide Info
X!Tandem Output Field PepXML Field Comments
./protein[1]/label ./spectrum_query/search_result/search_hit/protein

./protein[1]/uid Not found
./protein[1]/peptide[1]/domain[1]/id Not found
maxI Not found
fI Not found
./protein[1]/id ./spectrum_query/start_scan

./protein[1]/peptide[1]/domain[1]/start Not found
./protein[1]/peptide[1]/domain[1]/end Not found
./protein[1]/peptide[1]/domain[1]/expect ./spectrum_query/
search_result/search_hit/search_score[5]/value

./protein[1]/peptide[1]/domain[1]/mh Not found
./protein[1]/peptide[1]/domain[1]/delta ./spectrum_query/search_result/
search_hit/massdiff

./protein[1]/peptide[1]/domain[1]/hyperscore ./spectrum_query/
search_result/search_hit/search_score[1]/value

./protein[1]/peptide[1]/domain[1]/nextscore ./spectrum_query/
search_result/search_hit/search_score[2]/value

./protein[1]/peptide[1]/domain[1]/y_score ./spectrum_query/
search_result/search_hit/search_score[4]/value

./protein[1]/peptide[1]/domain[1]/y_ions Not found
./protein[1]/peptide[1]/domain[1]/b_score ./spectrum_query/
search_result/search_hit/search_score[3]/value

./protein[1]/peptide[1]/domain[1]/b_ions Not found
./protein[1]/peptide[1]/domain[1]/pre ./spectrum_query/search_result/
search_hit/peptide_prev_aa

./protein[1]/peptide[1]/domain[1]/post ./spectrum_query/search_result/
search_hit/peptide_next_aa

./protein[1]/peptide[1]/domain[1]/seq ./spectrum_query/search_result/
search_hit/peptide

./protein[1]/peptide[1]/domain[1]/missed_cleavages ./spectrum_query/
search_result/search_hit/num_missed_cleavages



PTM Info
X!Tandem Output Field PepXML Field Comments
./protein[1]/label ./spectrum_query/search_result/search_hit/protein

./protein[1]/uid Not found
./protein[1]/id ./spectrum_query/start_scan

./protein[1]/peptide[1]/domain[1]/aa/type /search_summary/
aminoacid_modification/aminoacid These amino acid changes are located
on only one area in the PepXML file unlike in the X!Tandem version
where they are spread out in various nodes.
./protein[1]/peptide[1]/domain[1]/aa/at Not found
./protein[1]/peptide[1]/domain[1]/aa/modified /search_summary/
aminoacid_modification/massdiff
./protein[1]/peptide[1]/domain[1]/aa/pm Not found
./protein[1]/peptide[1]/domain[1]/seq ./spectrum_query/search_result/
search_hit/peptide

[Edwin Mulwa]

Hi,

I have recently converted an X!Tandem output file to PepXML format using Tandem2XML utility. The X!Tandem output file was generated from an MGF file. After the conversion, I compared the contents of the X!Tandem output and PepXML files to try to determine which attributes in the PepXML file represent related attributes in the X!Tandem output file. It seems that not all attributes that we deem important (for a project we are doing) in the X!Tandem output are represented in the PepXML file.

The crucial question is: What attributes in the X!Tandem output file are NOT represented in the PepXML file? I have attached a document that shows what we have in the X!Tandem file and the perceived equivalent in the PepXML file. Kindly help me determine if my comparison is correct and what I may be missing (Not Found) in PepXML format that actually exists.

Also,  how do the MASCOT output files compare to PepXML files? Does the same issue of “missing” attributes also exist?

Thanks in advance.

 

===============================================================

Edwin Mulwa

VP, Research & Development

Integrated Analysis, Inc.

"Making Sense of Data" TM

 

5446 Alta Vista Rd., Bethesda, MD 20814

office: 301-760-4906 |   fax: 301-560-6507

e-mail: emu...@integratedanalysisinc.com or emu...@i-a-inc.com

Website: www.i-a-inc.com

===============================================================

 

--
===============================================================
Edwin Mulwa
VP, Research & Development
Integrated Analysis, Inc.
"Making Sense of Data" TM

5446 Alta Vista Rd., Bethesda, MD 20814
office: 301-760-4906 |   fax: 301-560-6507
e-mail: emu...@integratedanalysisinc.com or emu...@i-a-inc.com
Website: www.i-a-inc.com
===============================================================