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m/z and CCS recalibration Bruker timsTOF files

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m/z and CCS recalibration Bruker timsTOF files Felina H.  2023-11-14 08:19
 

Dear Skyline Team,

I am analyzing lipids using a timsTOF Pro. The Bruker PASEF-timsTOF files were recalibrated using Data Analysis (Bruker) after measurement.
Is there any possibility to retrace whether Skyline is using the recalibration after measurement or the calibration that was done before the measurement both for the m/z values as well as for the ion mobility dimension?
I compared both files (no recalibration called "raw" and the recalibrated one called "recal") and could not observe any differences which led me to the assumption that Skyline is not using the recalibration. However, I would need to work with the recalibrated data.
Could you clarify for me if Skyline is able to access the recalibration or not? And if it is possible, how to ensure that it took the recalibration?

I uploaded a Skyline file containing the raw file and the recalibrated file (raw_vs_recal_C13_50uL_neg.sky.zip) and the data files (data_tims_calibration.zip).

Thanks for your help!

Best,
Felina
 
 
Brian Pratt responded:  2023-11-14 09:12

Hi Felina,

Skyline will always use the calibration embedded in the file for conversion from CCS to ion mobility.

But in the provided document Skyline hasn't been given any CCS information so no ion mobility values have been used in chromatogram extraction.

Even so, it's unlikely that the recalibration is going to change the conversion values very much.

Thanks for using the Skyline support board,

Brian Pratt
 
Brian Pratt responded:  2023-11-14 12:16

I also notice that a comparison of the two files shows no differences other than in the desktop.ini file, so either the recalibration resulted in no changes, or it wasn't actually updated in the file. But I don't know anything about how that process works.