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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/7cb42706-53ae-4c94-acd2-ea0293fea8b2n%40googlegroups.com.
