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-discuss+unsubscr...@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-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D_yH%3DQ_Q3oRBEH3O12VmKkTGFPJ37y0ho2CewGSqh9SiQ%40mail.gmail.com.
