Difference in how modified AA are reported

[GATTACA]

Hi guys,

I was looking at the pep.xml file generated by the latest release of Comet and noticed an inconsistency from other pep.xml files generated for Mascot results (for example).
Normally the top of the file lists the modifications used in the search results.
Traditionally these elements report the mass of the modified residue. But in comet the elements just report the mass of the residues unmodified.

Example from Comet-derived pep.xml:
 <aminoacid_modification aminoacid="M" massdiff="15.9949" mass="131.0405" variable="Y" symbol="*"/>
 <aminoacid_modification aminoacid="S" massdiff="79.9663" mass="87.0320" variable="Y" symbol="#"/>
 <aminoacid_modification aminoacid="T" massdiff="79.9663" mass="101.0477" variable="Y" symbol="#"/>
 <aminoacid_modification aminoacid="Y" massdiff="79.9663" mass="163.0633" variable="Y" symbol="#"/>
 <aminoacid_modification aminoacid="C" massdiff="57.0215" mass="160.0306" variable="N"/>


In Mascot-derived pep.xml:
<aminoacid_modification aminoacid="M" mass="147.035400" massdiff="15.994915" variable="Y"/>
<aminoacid_modification aminoacid="S" mass="166.998359" massdiff="79.966331" variable="Y"/>
<aminoacid_modification aminoacid="T" mass="181.014010" massdiff="79.966331" variable="Y"/>
<aminoacid_modification aminoacid="Y" mass="243.029660" massdiff="79.966331" variable="Y"/>
<aminoacid_modification aminoacid="C" mass="160.030649" massdiff="57.021464" variable="N"/>

I'm not sure if this is a bug or simply a difference in how the search engine results are reported.

Any thoughts?
Damian

[Jimmy Eng]

Damian,

See this post:  https://groups.google.com/forum/?fromgroups=#!topic/comet-ms/KrbM57S050M

--
You received this message because you are subscribed to the Google Groups "spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discu...@googlegroups.com.
To post to this group, send email to spctools...@googlegroups.com.
Visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

[GATTACA]

Yet another example of why I should search the discussion board *before* posting a question! :)

Thanks Jimmy. :)