Here is my condition.xml file: Thanks.
<SUMmOnCondition description="TMT-6plex">
<fragmentMasses>
<reagent mz="126.127725">
<reagent mz="127.124760">
<reagent mz="128.134433">
<reagent mz="129.131468">
<reagent mz="130.141141">
<reagent mz="131.138176">
</fragmentMasses>
<isotopicContributions>
<contributingMz value="1">
<affected mz="2" correction="-2"/>
</contributingMz>
<contributingMz value="2">
<affected mz="1" correction="-2"/>
<affected mz="3" correction="-2"/>
</contributingMz>
<contributingMz value="3">
<affected mz="2" correction="-2"/>
<affected mz="4" correction="-2"/>
</contributingMz>
<contributingMz value="4">
<affected mz="3" correction="-2"/>
<affected mz="5" correction="-2"/>
</contributingMz>
<contributingMz value="5">
<affected mz="4" correction="-2"/>
<affected mz="6" correction="-2"/>
</contributingMz>
<contributingMz value="6">
<affected mz="5" correction="-2"/>
</contributingMz>
</isotopicContributions>
<massTolerance value="0.02"/>
<centroiding type="2" iterations="1"/>
<normalization type="1"/>
<targetMs level="2"/>
<output type="1"/>
<quantitationFile name="quantitation.tsv"/>
<minimumThreshhold value="20"/>
</SUMmOnCondition>
On Wednesday, July 10, 2013 3:08:36 PM UTC-5, [email protected] wrote:
>
> Hi there,
> I am pretty new to TMT quantitation. Apologies if my questions are too
> naive.
>
> I am recently tackling iodoTMT6plex labeling on Cys. Libra algorithm,
> originally designed for itraq labelled at N term and Lys, is claimed to be
> also suitable for TMT on TPP wiki page. So I assume that labkey would also
> be capable of handling my situation. However, there is limited introduction
> to the Libra, and the main one:
>
> http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/src/Quantitation/Libra/docs/libra_info.html
>
> is pretty out of date. I generated the condition.xml file as attached file
> pretty much as indicated this page. My questions are:
>
> 1. can anybody help me look into the condition.xml file to see if there is
> any problem?
>
> 2. TPP wiki pages says:
> "If you would like to generate a condition.xml file, please use
> http://db.systemsbiology.net/webapps/conditionFileApp/";. But the link is
> dead already. Can anybody update the link possibly?
>
> 3. Our TMT is labeled on Cys; so for a lot of identified peptides, if they
> don't have a cys, then it shouldn't display the quant information for that
> peptide. Thermo's proteome discoverer deals with this very good. However,
> when I tried TPP Libra, it gives all quant information even if that peptide
> does not have Cys. I guess I have to program to get rid of these fake quant
> information and re-assemble the protein quantitation offline. With that
> being said, Is there automatic way or update to automate this process? I am
> using TPP 4.5 right now.
>
> Thanks for any input in this thread! You guys are awesome to make
> beautiful stuff happening.
>
--
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.
For more options, visit https://groups.google.com/groups/opt_out.
