Comparing MS1 data with and without FAIMS

Comparing MS1 data with and without FAIMS paul.derbyshire  2024-02-15 04:07

Hi Skyline team,

I've been running some samples on two different Thermo mass specs - Orbitrap Fusion and Orbitrap Eclipse with FAIMS. When I build the data in Skyline I see distinct saw-tooth chromatograms from Eclipse/FAIMS samples but not from Fusion samples (see attached screenshots). Applying smoothing masks the saw-tooth appearance. Is this a effect of the FAIMS ion separation or is there something in transition settings that needs to be applied before data import?

Thanks in advance.

Paul Derbyshire

Nick Shulman responded:  2024-02-15 06:23
Jagged chromatograms like that indicate that the chromatogram was extra from two different sorts of spectra.
Yes, with FAIMS data you would expect to see jagged chromatograms like that, and you do not want that and you should fix it by telling Skyline the correct compensation voltage to use for each precursor.

I am not sure exactly what the best way is to tell Skyline the compensation voltage values for your precursors. You might be able to do something involving creating an ion mobility library at "Settings > Transition Settings > Ion Mobility"
Or you might use the Document Grid to set the "Explicit Compensation Voltage" values for each of your precursors.

After you have told Skyline about the CV values you should tell Skyline to extract chromatograms again by using the "Reimport" button at "Edit > Manage Results".

You might find some useful information on the Ion Mobility tutorial page, although FAIMS is different from the other sorts of ion mobility separation, so I'm not sure how well FAIMS is covered there:
-- Nick
Brian Pratt responded:  2024-02-15 10:31
The easiest way is to work with FAIMS us to use an ion mobility library, and to create that library by having Skyline determine the best compensation voltage for each precursor with the "Use Results" button.

Settings > Transition Settings > Ion Mobility > Ion Mobility Library > Add > Use Results
and set
Settings > Transition Settings > Ion Mobility > Ion Mobility Library > Window Type > Fixed
with any value greater than zero.

Re-import the raw data after that, and the sawtooth will go away.