quick question feature description Tobi  2020-04-02
 

Dear all,

https://skyline.ms/_webdav/home/software/Skyline/@files/tutorials/DIA-2_6.pdf

can you please help me with a quick explanation? In the link above, it is said "DIA precursor window for exclusion tells Skyline not to include transitions that fall in the DIA isolation window".

In the current Skyline daily, the pop-up tool-tip says you can change between symmetric and setting-based exclusion windows, and contrary to the above it is phrased as if now some kind of exclusion is applied in any case.

What is the current function of checking/unchecking this feature? The Tutorial and text next to checkbox indicate a On/Off function while the pop-up tool-tip indicates On-variant A / On-variant B.

Looking forward to get a short help on this.

With best wishes,
tobi

 
 
Nick Shulman responded:  2020-04-02

The tooltip for the "Use DIA precursor window for exclusion" says:

If checked, the precursor exclusion window is taken from the Full-Scan settings instead of being symmetric around the precursor m/z. This is recommended for DIA/SWATH data.

Skyline only allows you to check the checkbox if your MS2 full scan acquisition method is "DIA" and you have prespecified the isolation windows and your isolation scheme has specified the window width (i.e. you did not choose "Results Only").

If your acquisition method is not DIA, then Skyline does not show you the "Use DIA precursor window" checkbox. Instead, Skyline shows you a textbox called "Precursor m/z exclusion window" where you are supposed to type in a number.

The tooltip for the "Precursor m/z exclusion window" textbox is:

A m/z window around the precursor m/z within which transitions are excluded, or blank. A window of 20 will exclude all transitions within 10 on either side of the precursor m/z.

So, the "instead of being symmetric" part of the first tooltip isn't saying that the checkbox toggles between symmetric and asymmetric. It's trying to make a distinction between the behavior that the checkbox is offering, versus what would happen if you typed a number into the textbox. This is a little confusing since there has never been a case where Skyline would be showing checkbox and the textbox at the same time.
-- Nick

 
Tobi responded:  2020-04-03

Thank you very much for the explanation, now it makes sense.

With best wishes,
tobi