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Bruker timsTOF HT ion mobility filtering resolving power

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Bruker timsTOF HT ion mobility filtering resolving power chloe baldreki  2024-11-28 08:17
 

I'm very new to Skyline and am trying to set up my project for some DIA data collected on a Bruker timsTOF HT. In doing so I have a few questions...

  1. When configuring the full-scan settings, is it best to use the resolving power that is stated by Bruker for this instrument (60,000)? I ask as I read in another post that the resolution setting in Skyline is used to define the width of the XIC extraction, and if in MS1 it is set a little lower than the instruments stated resolution, it can account a bit better for potential mass accuracy deviation. If going a little lower is useful, do you have any suggestions on what this should be?
  2. How do I determine what the ion mobility filtering resolving power should be? Is this something I should be able to ascertain from my data?
    Thank you for your help!
 
 
Brian Pratt responded:  2024-12-02 13:19

Hi Chloe,

I don't have specific suggestions for values - I'd say the best thing is to do a chromatogram extraction in Skyline starting with the nominal instrument resolving power, then click on the chromatograms to see the mz/mobility/time heatmap to determine a reasonable resolving power for the mobility dimension, and possible adjustment to the value used in the m/z dimension.

Thanks for using the Skyline support board,

Brian Pratt