Optimizing FAIMS on new Thermo instruments

Optimizing FAIMS on new Thermo instruments Martijn van Duijn  2019-09-18


Our institution acquired a shining new Orbitrap Eclipse with a FAIMS source module. The FAIMS module need optimization for targeted analysis of our analytes, in order to obtain the best compensation voltage for transmission of the ion of interest.

It would be great if Skyline could facilitate this optimization step, similar to the optimization of collision energies that is already done. In fact, Skyline already seems to include a very similar optimization feature "Compensation Voltage', which seems to be intended for use with the SciEx Differential Mobility Separation. Can this feature be adapted to be used with Thermo FAIMS Compensation Voltages, or is this something that is intended for implementation in a future release of Skyline?


Martijn van Duijn

Brian Pratt responded:  2019-11-20

Hi Martjin,

Sorry for the slow response.

Can you please have a look at this request


and see if you are both looking for the same capability?



Martijn van Duijn responded:  2019-11-20

Hi Brian,

It seems Erik is asking for importing existing data acquired with multiple CV, and my request is also about exporting a method for finding an optimal CV for a target peptide, and plotting the outcome after importing result files, like it is done for collision energies.

The number of CV steps that are sensible to test in FAIMS are less than collision energy levels. It may be overkill to make an export feature generate methods that test various CV levels. If we generate the method manually then my question reduces to Erik's..

Brian Pratt responded:  2019-11-20

OK, let's start with making sure that we can at least do the "choose best available CV" part of this.



philip remes responded:  2020-10-09

I am also hoping that the FAIMS CV could be optimized in the same way that collision energy can, this would be really nice. I see that as of build it isn't possible still.