Increase in m/z of fragment ions when exporting methods for collision energy optimisation sarah lennon  2020-03-24

Dear Skyline team,

I have just noticed that when exporting a Waters method for collision energy optimisation from Skyline Daily, the m/z of the fragment ion is increased slightly (+0.01 Da, +0.1 Da from first to last) with increased collision energy. Is there any reason for that ?

Thank you very much for your help,
Kind regards,


Brian Pratt responded:  2020-03-24

Hi Sarah,

That's normal - Skyline has to introduce that variation so that the mass spec can be made to apply different CE values to the same transition within a single method. If they all had the same Q1/Q3 values the machine wouldn't know what to do with the varying CE values.

Thanks for using the Skyline support board!

Brian Pratt

sarah lennon responded:  2020-03-24

Hi Brian,

Thank you very much for your answer ! Ah yes I see, I did not think about that !