Different retention times for heavy and light from

Different retention times for heavy and light from Martin Eisinger  2020-06-23


I know the topic has been discussed several time but I didn't find a conclusive answer. I work with small molecules and use fully deuterated versions as internal standards. The deuteration leads to a considerable RT shift between heavy and light form. However if I define them as heavy and light in my transition list, skyline uses the same integration boundaries for both forms. The only solutions I found to overcome this problem is to set very wide integration boundaries, so that both peaks heavy and light are covered. It's ok but no perfect solution as in that case a lot of baseline is also integrated.

Is there any good way of telling Skyline that heavy and light RTs don't have to match and allowing it to use different integration boundaries for both forms?

Thanks in advance!



Brian Pratt responded:  2020-06-23

Hi Martin,

You may wish to define the deuterated version as its own molecule, then use Skyline's "Surrogate Standards" capability to associate them. The Skyline High Resolution Metabolomics tutorial covers this.

Thanks for using the Skyline support board,

Brian Pratt

Martin Eisinger responded:  2020-06-26

Thanks for the quick response!