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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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Instrument not detected, how to specify? #1642

Closed BjoernZiehr closed 3 months ago

BjoernZiehr commented 3 months ago

In the log I find: " If a different instrument was used, specify using '--instrument' via the command line or 'instrument=' in the param file."

but I'm unsure how to do this

yes I will upload

fcyu commented 3 months ago

Can you upload the log file?

Thanks,

Fengchao

BjoernZiehr commented 3 months ago

log_2024-06-21_15-29-10.txt

fcyu commented 3 months ago

Thanks for the log file. That warning message was from MSBooster, and it should not affect your result much. I think you could ignore it for now.

2024-06-21 15:28:54 [INFO] - Could not detect instrument type. Setting to Lumos. If a different instrument was used, specify using '--instrument' via the command line or 'instrument=' in the param file.

Hi @yangkl96 , I thought I have encoded the instrument type in the _uncalibrated.mzML. Not sure why MSBooster still complains about it. We can discuss about it when you have time.

Thanks,

Fengchao

BjoernZiehr commented 3 months ago

Ok thank you

yangkl96 commented 3 months ago

Yes this only matters if you are using a spectral prediction model that cares about the instrument type, but you are using DIA-NN for prediction, which does not.

@fcyu MSBooster searches for certain strings in the mzml metadata to determine instrument type. It is possible what MSFragger writes is not included in the list of strings that are considered, or not in the same metadata fields. We should discuss when I am back