Collision Energy Optimisation on TimsTOF Bruker

Collision Energy Optimisation on TimsTOF Bruker karweens jean  2022-05-03

Dear Skyline Team,
I am using a Bruker TimsTOF for proteomic analysis in PRM-PASEF mode and I would like to use the skyline software to optimize the collision energies of the produced ions. I have created a file taking into account the different collision energies to test per ion.

The acquisition went well and I managed to import the file on skyline.

However, skyline refuses to display the full histogram for the different collision energies tested.

I would like to know if it is possible to optimize collision energies with a TimsTOF file on skyline.

Thank you very much for your help,
Kind regards,


Nick Shulman responded:  2022-05-03
My understanding is that Skyline cannot do this sort of collision energy optimization with PRM data. Skyline only knows how to do this with SRM data.

When Skyline exports an SRM transition list for CE optimization, Skyline exports a series of transitions which all have the same Q1 value, and where the Q3 value differs by 0.01 units. But this is something that Skyline can only do for SRM data.

The analogous sort of thing for PRM, where the precursor m/z is changed by 0.01 units is not something that Skyline does, and is not something that Skyline would pay attention to when extracting chromatograms from PRM data.
-- Nick
karweens jean responded:  2022-05-04

Thank you very much for your answer! Do you plan to add this option in the next updates.