Skyline only allows you to choose precursor masses whose predicted abundance is at least 1%.
So, even though you have the correct setting on:
Settings > Transition Settings > Full Scan > MS1 filtering > Isotope Peaks Included
Skyline is not going to give you 4 precursor transitions if the molecule is not large enough that it has 4 different masses with an abundance above 1%.
May I ask why you want chromatograms for these low abundance isotopes? Is it to help with distinguishing the molecule from something else whose mass is maybe 1 Dalton different from what you are looking for?
Skyline does allow you to add the M-1 precursor. To do this, select a precursor in the Targets tree and choose the right-click menu item "Pick Children", and then click the button that looks like a funnel to turn off filtering, and then you can choose the M-1 transition. That transition can be useful for distinguishing molecules that differ by one Dalton. (I don't know how to add the M-1 transition to all of the precursors in your document-- I think you might have to do it one at a time like this).
I am not sure how having the M+2 transition or M+3 transition on such a small molecule would be helpful, but if it is, I could imagine us making that possible in a future version of Skyline.
- Nick |