fcyu
commented
1 week ago First of all, I need to clarify that the combined_site_*.tsv reports are generated by IonQuant for the MS1-based quant. There are no TMT intensities in that file. For the TMT workflow, please use the reports in the tmt-report folder.
To make IonQuant generated combined_*.tsv files, you need to specify the experiment groups in the workflow tab.
It seems the combined_site_K is the only file where I can find all modification sites and PTMprophet probabilities for each.
Such information is also in psm.tsv
Best,
Fengchao
lxavierneves
Log file: log_2024-09-25_14-48-40.txt
Description Hello, I've trying to analyse ubiquitination on K-GG enriched samples prepared using on-beads TMT labeling protocol, so I'm loading the TMT16_ubiquitination-K_tmt_or_ubiq workflow, but I'm not seeing the "combined_site_K_114.0429.tsv" file in the output folder. My input files are bRP fractions so I left Experiment and Bioreplicate columns blank so the fractions merge during search and TMT quantification.
PTMProphet is active and +114 is indicated as it should be.
I understand that TMT Integrator will generate the multi-site and single-site reports but shouldn't the "combined_site_K_114.tsv" be generated as well? It seems the combined_site_K is the only file where I can find all modification sites and PTMprophet probabilities for each.
A last note, the isotope error for this workflow is 0/1/2 whereas for other tmt workflows it can be -1/0/1/2, for example. Is it advised to keep 0/1/2?
Many thanks, Leandro