Hello Shagun,
Thank you for sharing your complete dataset. I still found the following
in the conditions file you included:
TMT10_VB297695_condition.xml
<massTolerance value="0.2" />
This should be set to 0.001 for this analysis to work on your type of
label. I am attaching the condition file with this change included so you
can rerun Libra using the condition file attached. Please make sure the
tolerance is correct in the file when you try running Libra again and if
you still see a problem please provide your TPP results interact* files
etc...
Cheers,
-David
On Fri, Apr 1, 2022 at 10:03 PM Shagun Gupta <sg2...@cornell.edu> wrote:
> The zip folder for the files can be found here:
> https://drive.google.com/drive/folders/1hnR2igUXM_K-Pld2xspikeu_xnLGUdMc?usp=sharing
>
> Let me know if you have any issues.
>
> Best
> Shagun
>
> On Friday, March 25, 2022 at 1:34:57 PM UTC-4 David Shteynberg wrote:
>
>> Please place your files on a shared drive and send me a link.
>>
>> On Fri, Mar 25, 2022 at 10:34 AM Shagun Gupta <sg2...@cornell.edu> wrote:
>>
>>> Hi David
>>>
>>> Could you suggest a good email to reach you with? I can share the
>>> pep.xml's and Libra condition file that way?
>>>
>>> -Shagun
>>>
>>> On Friday, March 25, 2022 at 11:00:38 AM UTC-4 David Shteynberg wrote:
>>>
>>>> Hello Shagun,
>>>>
>>>> Thank you for your email and interest in the TPP. I have recently been
>>>> comparing TMTPro analysis by ProteomeDiscoverer and Byonic to that produced
>>>> by TPP's Libra. As far as I can tell, when I run and compare the
>>>> quantities (intensities) they are mostly the same between Libra (without
>>>> isotopic impurity correction and 0 pseudocounts) and the
>>>> ProteomeDiscoverer/Byonic. Execution of Libra is defined in the
>>>> conditions.xml file that has to be defined for each Libra run. I would be
>>>> happy to take a look at your data and analysis to see if it can be placed
>>>> on the right path for the Libra analysis to work. Please post your results
>>>> somewhere I can download and test.
>>>>
>>>> Cheers,
>>>> -David
>>>>
>>>> On Fri, Mar 25, 2022 at 6:36 AM Shagun Gupta <sg2...@cornell.edu>
>>>> wrote:
>>>>
>>>>> Hello
>>>>>
>>>>> Our lab has been trying to use Libra to quantify MS2 (Ion-trap)
>>>>> identification and MS3-based quantification of TMT datasets and we were
>>>>> trying to benchmark with an artificial yeast and mammalian spiked dataset
>>>>> with known fold-change (FC) values. However we observe drastically
>>>>> different values than expected, something we don't observe with other
>>>>> search engines for the same dataset.
>>>>>
>>>>> Has this issue been encountered before/ is there something obviously
>>>>> wrong when running with TPP that might cause this? Happy to provide
>>>>> further
>>>>> details on the dataset and parameters used to run with (most of them
>>>>> default apart from additions like static modification for TMT and
>>>>> specification of MS3 for quantification among others).
>>>>>
>>>>> Thank you,
>>>>> Shagun
>>>>>
>>>>> --
>>>>> 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 view this discussion on the web visit
>>>>> https://groups.google.com/d/msgid/spctools-discuss/ce2c75fb-2da1-4e05-8d08-bbe5a30b0495n%40googlegroups.com
>>>>> <https://groups.google.com/d/msgid/spctools-discuss/ce2c75fb-2da1-4e05-8d08-bbe5a30b0495n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>>> .
>>>>>
>>>> --
>>> 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 view this discussion on the web visit
>>> https://groups.google.com/d/msgid/spctools-discuss/7a0b1188-7c5f-4528-9e90-282b860e7627n%40googlegroups.com
>>> <https://groups.google.com/d/msgid/spctools-discuss/7a0b1188-7c5f-4528-9e90-282b860e7627n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>> --
> 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-discuss+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/spctools-discuss/4d2752de-2e7d-46fe-be38-5700043ca984n%40googlegroups.com
> <https://groups.google.com/d/msgid/spctools-discuss/4d2752de-2e7d-46fe-be38-5700043ca984n%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
>
--
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-discuss+unsubscr...@googlegroups.com.
To view this discussion on the web visit
https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D-RdTDUTdOGWGDK%3DwhqwSZNGDgc5KVmDrmXsfqYe_C4%2Bg%40mail.gmail.com.
<?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" />
</fragmentMasses>
<isotopicContributions>
<contributingMz value="1">
<affected mz="3" correction="0.074" />
<affected mz="5" correction="0" />
</contributingMz>
<contributingMz value="2">
<affected mz="4" correction="0.062" />
<affected mz="6" correction="0" />
</contributingMz>
<contributingMz value="3">
<affected mz="1" correction="0.008" />
<affected mz="5" correction="0.065" />
<affected mz="7" correction="0" />
</contributingMz>
<contributingMz value="4">
<affected mz="2" correction="0.004" />
<affected mz="6" correction="0.066" />
<affected mz="8" correction="0" />
</contributingMz>
<contributingMz value="5">
<affected mz="1" correction="0" />
<affected mz="3" correction="0.015" />
<affected mz="7" correction="0.056" />
<affected mz="9" correction="0" />
</contributingMz>
<contributingMz value="6">
<affected mz="2" correction="0" />
<affected mz="4" correction="0.016" />
<affected mz="8" correction="0.054" />
<affected mz="10" correction="0" />
</contributingMz>
<contributingMz value="7">
<affected mz="3" correction="0" />
<affected mz="5" correction="0.027" />
<affected mz="9" correction="0.047" />
</contributingMz>
<contributingMz value="8">
<affected mz="4" correction="0" />
<affected mz="6" correction="0.024" />
<affected mz="10" correction="0.044" />
</contributingMz>
<contributingMz value="9">
<affected mz="5" correction="0" />
<affected mz="7" correction="0.033" />
</contributingMz>
<contributingMz value="10">
<affected mz="6" correction="0.008" />
<affected mz="8" correction="0.029" />
</contributingMz>
</isotopicContributions>
<massTolerance value="0.001" />
<centroiding type="2" iterations="1" />
<normalization type="-1" />
<reporterFromMS3 value="1" />
<output type="1" />
<quantitationFile name="quantitation.tsv" />
<minimumThreshhold value="0" />
</SUMmOnCondition>
