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-discuss+unsubscr...@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/CAGJJY%3D-xO3RdbHi6_SN4gVj-uEJ4vQcPGPX%2Bx4DTegF1UM101g%40mail.gmail.com.
