Skyline transition settings for DIA with Waters MSe SONAR

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Skyline transition settings for DIA with Waters MSe SONAR christophef  2018-08-15 08:47
 

Dear Skyline users,

Can someone help me with understanding and choosing the right settings to process Waters DIA data acquired in MSe with SONAR option?
So far, I was always using Acquisition method: DIA with Isolation scheme: All Ions, when using Waters MSe data.

I have recently added SONAR acquisition mode: Quadrupole scan, 400-900 m/z with 50 Da windows, which means according to Waters terminology, 200 bins/500 Da * 50 = 20 bins.

I was wondering if I need to process this data as SWATH (with windows of 20Da) or still as All ions?
The "SWATH" approach does not seem to work in extracting MSMS data.

Any recommendation or confirmation about the isolation scheme to chose in SKYLINE?

Thanks in advance for your help

Christophe Folly

 
 
Brendan MacLean responded:  2018-08-15 09:12

Hi Christophe,
You still want the "All Ions" setting. The spectra are still presented to Skyline in a way that is indistinguishable to us from HDMSe and Skyline still treats the extra dimension as if it were "Drift Time". This is what Waters asked us to do over a year ago, and they still haven't given us software support for calibrating the high energy bins to precursor m/z values.

You will also want to check "Use spectral library ion mobility values when present" and "Linear peak width". Unfortunately, that is where my knowledge runs out and I am not sure how to recommend you set the "Width at im0" and "Width at imMax" values. I will ask Brian Pratt, the developer on this feature, to reply to this thread and also write a Tip about achieving this setup. But, I have at least described the general direction. You may want to contact Waters directly. We know they have done it and the more their customers contact them about it the more likely they are to put extra effort into providing us the necessary software to calibrate this dimension in terms of precursor m/z.

Thanks for posting to the Skyline support board.

--Brendan

 
christophef responded:  2018-08-15 09:51

Thanks Brendan for the quick answer.

I definitely need to figure out what the parameters about "spectral library ions mobility" have on the outcome. It is not clear to me at the minute.
It would be nice to have any additional information from Brian.
I will also contact Waters for more information regarding using Skyline and SONAR, as used in their applications notes.

Thanks again for your support

Best,
-Christophe