Collision Energy Optimization Small Molecules

Collision Energy Optimization Small Molecules klemens froehlich  2022-05-18

Dear Skyline Developers,
First of all thank you very much for your continued support and an amazing software package!

We are currently starting to use Skyline for small molecule projects.
I know that Skyline can do collision energy optimizations for SRM type experiments using transition list method export as described in a tutorial.

However, we only have high resolution instruments (orbitraps) in our lab and would like to do PRM of small molecules.

Accoding to this thread:
Skyline cannot do collision energy optimization for PRM data.

Now my question is:
Wouldn't it make sense to optimize the collision energy for small molecules even if we are using PRM? For example if I go to a publication where a compound was measured on a machine that uses a different type of fragmentation and I do not know in what range my collision energy would be optimal?
Or if only one transition is reported in a SRM experiment and I want to make sure to get the best sensitivity from my orbitrap machine for this transition?

Of course I can use more transitions in PRM but for small molecules I think that collision energy optimization is more important as you often only use one or two transitions as compared to pptide quantitation where you use more transitions.

Would it be possible to integrate PRM collision energy optimization somehow in Skyline?
Maybe by shifting the transition mass also by 0.0001 instead of 0.01 as for SRM experiments?

Best, Klemens

Brendan MacLean responded:  2022-05-18

Hi Klemens,
It does make sense, and it has been on our list for a while now. I hope we can have it working for you and others sometime this year, but I always hesitate to make promises when something is not receiving our active attention. Kaipo on the team started working on it last year, but then got pulled away to other higher priority issues.

Thanks for bringing it up again. Hearing from people who really want something always helps us prioritize.


klemens froehlich responded:  2022-05-19

hi Brendan,

Thank you for your reply.
I totally understand that this is not at the top of the priority list.

I will then do a workaround and split each collision energy setting into an own measurement, so that I can at least directly compare fragment intensities between replicates (and therefore collision energies).
I will have to write down the ideal CEs manually though, won't I?

Best Klemens