Hello Rachel,
The only potential issue when making your own condition file is to make
sure that the isotopic impurity correction factors are correctly entered in
the matrix. You also have to add the 11th channel under the <reagent> and
<contributingMz> tags, but this should be straightforward.
We are adding TMT-11 support to TPP for the upcoming release, and I am
attaching a condition file that I just generated with the new code. You
are welcome to use it, in case you have not already created your own, but
please note that the isotopic impurity factors are likely to be different
-- please review these and correct if necessary. And please let me know if
you do use it and encounter any issues. We'd also like to know if it
works, since we have no data at our disposal to test!
Also, would you mind sharing the Themo Lot Number of your TMT-11 kit?
That way I can look up the latest impurity factors from its COA and put
them as defaults in Petunia. Feel free to email me directly if you prefer,
or to simply post those factors if you have them available.
Hope this helps!
--Luis
On Thu, Dec 20, 2018 at 12:46 PM Rachel Nadeau <[email protected]>
wrote:
> Hi all,
>
> I was hoping to use Libra for peptide quantification of TMT 11-plex data.
> Since there is no specific option to do this through the TPP graphical
> interface (i.e. creating condition.xml file), I was going to simply modify
> the Libra condition file. Should I expect any issues in doing this?
>
> Thanks,
>
> Rachel
>
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<?xml version="1.0" encoding="UTF-8"?>
<SUMmOnCondition>
<fragmentMasses>
<reagent mz="126.127726" />
<reagent mz="127.124761" />
<reagent mz="127.131081" />
<reagent mz="128.128116" />
<reagent mz="128.134436" />
<reagent mz="129.131471" />
<reagent mz="129.137790" />
<reagent mz="130.134825" />
<reagent mz="130.141145" />
<reagent mz="131.138180" />
<reagent mz="131.144499" />
</fragmentMasses>
<isotopicContributions>
<contributingMz value="1">
<affected mz="3" correction="0.05" />
<affected mz="5" correction="0" />
</contributingMz>
<contributingMz value="2">
<affected mz="4" correction="0.046" />
<affected mz="6" correction="0" />
</contributingMz>
<contributingMz value="3">
<affected mz="1" correction="0.006" />
<affected mz="5" correction="0.064" />
<affected mz="7" correction="0" />
</contributingMz>
<contributingMz value="4">
<affected mz="2" correction="0.004" />
<affected mz="6" correction="0.034" />
<affected mz="8" correction="0" />
</contributingMz>
<contributingMz value="5">
<affected mz="1" correction="0" />
<affected mz="3" correction="0.005" />
<affected mz="7" correction="0.032" />
<affected mz="9" correction="0" />
</contributingMz>
<contributingMz value="6">
<affected mz="2" correction="0" />
<affected mz="4" correction="0.007" />
<affected mz="8" correction="0.033" />
<affected mz="10" correction="0" />
</contributingMz>
<contributingMz value="7">
<affected mz="3" correction="0" />
<affected mz="5" correction="0.013" />
<affected mz="9" correction="0.029" />
<affected mz="11" correction="0" />
</contributingMz>
<contributingMz value="8">
<affected mz="4" correction="0" />
<affected mz="6" correction="0.013" />
<affected mz="10" correction="0.03" />
</contributingMz>
<contributingMz value="9">
<affected mz="5" correction="0" />
<affected mz="7" correction="0.015" />
<affected mz="11" correction="0.018" />
</contributingMz>
<contributingMz value="10">
<affected mz="6" correction="0" />
<affected mz="8" correction="0.021" />
</contributingMz>
<contributingMz value="11">
<affected mz="7" correction="0" />
<affected mz="9" correction="0" />
</contributingMz>
</isotopicContributions>
<massTolerance value="0.001" />
<centroiding type="0" iterations="1" />
<normalization type="1" />
<output type="1" />
<quantitationFile name="quantitation.tsv" />
<minimumThreshhold value="0" />
</SUMmOnCondition>
