Great! Thank you. On Wed, Apr 6, 2022, 7:04 AM Shagun Gupta <[email protected]> wrote:
> 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 > <https://groups.google.com/d/msgid/spctools-discuss/43abc423-6593-469a-9ca1-b1edbd7c4c58n%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/CAGJJY%3D_j4Kq0ghLQ9yieThn78N8S-Yrf_FDJv-LvSMwtXGjo3w%40mail.gmail.com.
