Collision Energy Optimization Thermo Fusion Lumos anne sanner  2021-02-25

Dear Skyline team,

I am currently setting up a PRM assay on the Thermo Fusion Lumos and would like to use Skyline's collision energy optimization function. In the default settings "Transition Settings -> Prediction -> Collision energy", there are only linear equations given for triple quads. Can you tell me what the regresison parameters for the Fusion Lumos are? Thank you!


Kaipo responded:  2021-02-25

Hi Anne,
CE optimization for PRM is not yet supported in Skyline, but something I am currently working on for the next release. Data files would be helpful for testing though, do you have any that you would mind sharing?


anne sanner responded:  2021-02-26

Hi Kaipo,
thanks for the reply. Will I be able to use the CE optimization option in Skyline for data analysis, even if I didn't set up the assay in Skyline but manually? That would be of real help. I unfortunately don't have any data files that I would be ready to share though, I'm sorry.


Brendan MacLean responded:  2021-02-26

Hi Anne,
We may have gotten confused by the mention of "optimization" in your request, which Kaipo is working on. However, the Thermo full-scan instruments (Orbitrap, ion trap) use normalized collision energy (NCE) and therefore usually do not require an equation for CE. They have their own equations embedded in the instrument software. This allows Skyline to mostly use a single NCE value for all peptides in a given method.

There may be ways to change this, but I am not entirely sure. There definitely will be once Kaipo's work is completed. Then it will be possible to perform CE optimization for PRM as we have described for SRM (see the CE Optimization tutorial -, and MacLean, Anal. Chem. 2010). Though, I am not clear that this is what you are seeking.

So, very short answer, for a Fusion Lumos, you generally do not need to worry about the CE setting in the Transition Settings - Prediction tab.

If you truly want to pursue optimized NCE values on a Lumos, let us know and we would be interested in having your feedback on that project currently underway.