Hello Yasir, Can you try re-running Libra without the centroiding option? (i.e. set type="0") Or are your mzML data not centroided? Another thing to try: are you able to open the PeptideProphet + Libra results in the PepXMLViewer? You should be able to see if there are a significant number of quantified PSMs -- you should also be able to examine a few individual spectra and zoom in on the reporter ion signals. Lastly, what version of TPP are you running?
Cheers, --Luis On Thu, Sep 8, 2022 at 12:02 PM Yasir Ahmed <yazah...@gmail.com> wrote: > Greetings, > > I'm having difficulty performing TMT quantification using Libra on a > 16-plex dataset. Basically, the "quantification.tsv" file that Libra > outputs only contains zeros for both peptides and proteins. The Comet > search runs just fine. I'm at a loss for where things are going wrong. The > Mass Spec facility used ProteomeDiscoverer for the quantification, and it > worked fine so the issue is not the raw data. > > My TPP run repository can be found here > <https://github.com/YazBraimah/TPP_TMT_proteomics_pipeline>, and the > "condition.xml" file for Libra—along with the Comet params file—is in the > "params" folder. The commands used to run the TPP processes can be found in > the file called "Snakefile". I'm happy to provide any additional > information needed to help troubleshoot this. Any pointers/advise would be > greatly appreciated. > > Cheers, > Yasir > > -- > 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/7cb42706-53ae-4c94-acd2-ea0293fea8b2n%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/7cb42706-53ae-4c94-acd2-ea0293fea8b2n%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/CACyS9bo%3DQxLBhn3H%2B7cg9pTKXu1Yp1bTLwb%2BfF%3DR4y%2BujoF%3DxQ%40mail.gmail.com.
