Tony,
As far as I'm aware, there's no simple way to accomplish what you want to
do i.e. there's no option or switch in the TPP tools to turn off the fixed
mod masses but leave the variable mod masses in the peptide string.
If this is just a question of getting rid of those fixed mod masses in the
viewer w/o worrying about any other negative side effects, you can
accomplish this by getting rid of the specific modification strings in the
underlying .pep.xml file. Here's one example ... your N15 masses might be
a little different depending on what search tool/masses you used.
Consider the peptide AARSM where the Methionine residue has a variable
modification for oxidation (similar to your phosphorylation). Here is the
corresponding modication_info element for that peptide:
<modification_info>
<mod_aminoacid_mass position="1" mass="72.034149"/>
<mod_aminoacid_mass position="2" mass="72.034149"/>
<mod_aminoacid_mass position="3" mass="160.089251"/>
<mod_aminoacid_mass position="4" mass="88.029063"/>
<mod_aminoacid_mass position="5" mass="148.032434"/>
</modification_info>
You would have to change this to:
<modification_info>
<mod_aminoacid_mass position="5" mass="148.032434"/>
</modification_info>
Leaving only the variable modification. When visualizing in the PepXML
Viewer, all of the numbers, except for variable oxidation, goes away. I'm
sure you don't want to manually delete thousands of lines in your pep.xml
file so you need to figure out how to do this automatically. If you are on
a linux system or have cygwin installed on a windows box, you can
accomplish this with something the following:
mv interact.pep.xml interact.pep.xml.bak
grep -v -f modslist.txt interact.pep.xml.bak > interact.pep.xml
The "-v" specifies an inverted match i.e. pull out lines that don't match
the expression. And the "-f modslist.txt" specifies the "modslist.txt"
file that contains the modification lines to pull out. A "modslist.txt"
file that I just tested for an N15 search contains the following (but you
should make sure these are the exact numbers you have in your pep.xml file):
mass="58.018499"/>
mass="72.034149"/>
mass="88.029063"/>
mass="98.049799"/>
mass="100.065449"/>
mass="102.044713"/>
mass="114.081099"/>
mass="116.023978"/>
mass="116.036997"/>
mass="130.039628"/>
mass="130.052647"/>
mass="130.089033"/>
mass="132.037519"/>
mass="140.050017"/>
mass="148.065449"/>
mass="160.089251"/>
mass="161.027683"/>
mass="164.060363"/>
mass="188.073383"/>
mass="327.121455"/>
Hope this puts you on the right track. Good luck!
- Jimmy
On Fri, May 24, 2013 at 3:02 PM, Tony Wang <[email protected]>wrote:
> Hi Everyone:
>
> I am processing 15N labeled peptides data with TPP. All of AA in the
> pep.xml have a number, making it very difficult to read the sequence AND
> to find variable modification such as phosphopeptides. I want to eliminate
> the numbers for fixed modification but keep the numbers for variable
> modification. Would anyone help me?
>
> Tony
> ******
>
> --
> 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 [email protected].
> To post to this group, send email to [email protected].
> Visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>
>
--
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 [email protected].
To post to this group, send email to [email protected].
Visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
For more options, visit https://groups.google.com/groups/opt_out.
