Hi David Apologies, for some reason my post that it all worked out never made it through. Instead one of my older replies I think got posted again. Sorry for the confusion and thank you for your help!
Shagun On Tuesday, April 5, 2022 at 3:09:59 PM UTC-4 David Shteynberg wrote: > 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 <[email protected]> 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 <[email protected]> >>> 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 <[email protected]> >>>>> 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 [email protected]. >>>>>> 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 [email protected]. >>>> >>> 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 [email protected]. >> > 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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/43abc423-6593-469a-9ca1-b1edbd7c4c58n%40googlegroups.com.
