No TMT channel columns in fragpipe

[calmnine]

• Describe the issue or question:

Hi. I ran TMT11-plex file using fragpipe. There's no TMT channel columns of intensity in protein.tsv. When I use fragpipe 21.1 with using msfragger 4.0 using sample file, workflow, manifest, there's a channel column in protein.tsv Is there any update in TMT quantification?

• Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

log_2024-03-04_16-50-33.txt

[fcyu]

Your log shows that MSFragger stopped due to not enough memory.

I guess you uploaded the wrong log file. What you did maybe use IonQuant, that only writes the intensity to psm.tsv, as the "intensity extraction tool". For TMT analysis, you'd better use the intensity tables in the tmt-report folder because they are normalized. If you still want to have the TMT intensity in the protein.tsv, you could switch the "IonQuant" to "Philosopher" in the "Quant (Isobaric)" tab.

Best,

Fengchao