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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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Settings influencing IonQuant intensity values #1900

Open eldenrowland opened 1 day ago

eldenrowland commented 1 day ago

- 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.)

- Describe the issue or question:

Hi Fragpipe team,

I'm looking for some clarification on Ionquant settings.

Specifically I would like to know how the retention time tolerance, rttol=0.4 min(default) influences peak picking. I am analyzing a long 3 hr run where the peaks widths are sometimes 1 min. Therefore, I adjusted the rttol to 1 min. Adjusting this setting quite drastically changes the intensity values. Am I thinking about this correctly?

I have read the ionquant paper but still wasn't sure about this particular setting.

All the best,

Elden Rowland

fcyu commented 1 day ago

It controls the max distance between an identified MS2 scan and the XIC's apex.

Best,

Fengchao

eldenrowland commented 5 hours ago

Hi Fengchao,

That's super helpful. So, if the rttol was set too low, and the peak apex was more than 0.4 min from the MS2 identification, then that peak would not be quantified? Or would the integrated peak be truncated?

Thanks very much,

Elden

fcyu commented 5 hours ago

It won't be quantified.

Best,

Fengchao