Variable MRM time windows

Variable MRM time windows benoit fatou  2020-11-13

Hi Skyline Team,

I was wondering if there is any way in Skyline to generate variable MRM time window for each peptide when exporting the method or transition list.
I am asking you because some of my peptides have a broad peak width so if I set a very short time window, I would crop them out. On the other hand, making a short time window for the peptides with very small peak width might increase their sensitivity because we decreased the number of concurrent transition pairs.

Let me know if you need more information or if you have any question.
Thanks for your help,
All the best,

Brian Pratt responded:  2020-11-13

Hi Benoit,

Skyline supports explicitly defined per-peptide retention time windows, defined by retention time and window width, which I think will give you what you want here.

You can set these values using the Document Grid: open the Peptides report, then Customize Report to add the Explicit Retention Time and Explicit Retention Time Window columns.

Thanks for using the Skyline support board!

Brian Pratt