No automatic pick children for isotopic envelope

support
No automatic pick children for isotopic envelope karamj33405  2025-06-23 11:17
 

For some analytes (PFAS/small molecule) Skyline is not automatically recognizing the M+1 and M+2 even though they are in high abundance (as shown in screenshot). Occasionally it will only show the M+1. Is there a setting I need to turn on to resolve this? Thanks!

 
 
Nick Shulman responded:  2025-06-23 12:13
In order to be able to choose the M+1 mass, the following all need to be true:
1. You have specified a chemical formula for your molecule.
2. The predicted isotope abundance of the M+1 mass is at least 1% of the most abundant mass.
3. The "Precursor mass analyzer" on the "Full Scan" tab at "Settings > Transition Settings" is not "QIT".

In addition, the "Isotope Peaks Included" setting on the Full Scan tab controls which masses Skyline gives you by default.

In your screenshot, you might actually be able to select the M+1 mass if you first click on the filter button. The filter button is the third button down on the left edge of the child picker window. The child picker window is the one that says "Compound 1_4 Precursors".

If the filter button is unselected, Skyline will allow you to choose any mass whose predicted abundance is at least 1% of the most abundant mass.
If the filter button is selected, then Skyline will only show you the subset of masses which also satisfy the "Isotope Peaks Included" settings on the Full Scan tab.

If you're still having trouble choosing the masses you want, you can send us your Skyline document.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files.

Files which are less than 50MB can be attached to these support requests.
You can always upload larger files here:
https://skyline.ms/files.url
-- Nick