Dynamic isolation windows for PRM

Dynamic isolation windows for PRM hober  2018-11-08

I have a minor question/suggestion, depending on if it's already implemented in Skyline or not.

When running PRMs, the early eluting peptides are the ones that experience the biggest drift in retention time. At the same time, most of the peptides that I'm interested in tend to elute closer to the middle of the gradient and be more stable RT-wise.
When setting the retention time window size, this results in a lot of "unused" potential for big windows at the beginning of the run, where the RT-drift is more evident, when using the same window sizes for all isolations.

Would it be possible to export isolation lists with dynamic window sizes?

If not, would it be possible to implement in some future version of Skyline?
You could in such case for example input a window size range that you would like to use and then let the windows be adjusted based on a "concurrent precursors cut-off".

Best regards
/Andreas Hober

Brendan MacLean responded:  2018-11-08

Hi Andreas,
We certainly thought about that in the early days of Skyline, but we never came up with a useful function to apply to create these variable window sizes. Maybe you can describe how you think this would work more precisely. I get the range idea, but not yet what function would be applied to choose the window size within the range.

Thanks for your feedback. With a clear useful description, we may be able to implement something to help.