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.
