Differnt product ions not shown together in Skyline FlorianBonn  2019-10-10
 

I have a strange problem with Skyline 19.1.0.193. I want to quantify a large peptide in a SRM experiment with a triple quad. The precursor is m/z ~700 with +4. We measured 3 product ions: b3 (m/z 350 +1), y19 (m/z 1050 +2) and y21 (m/z 760 +3) with a Qtrap and loaded the data in Skyline.
If I select all three Transitions it shows me data for y19 and y21, but for b3 only a zero signal. If I remove either y19 or y21 from the list, only data for b3 is there and for y19 or y21 only the zero signal is there. If I again add y19/y21 to the transition list, the b3 trace is gone and the two from the large ions are both displayed. Can anyone help me out to get all three transitions displayed at once or at least b3 and y19 together?
Sorry if this questions was answered, but search terms I tried were either to specific (nothing was found) or to general.

 
 
Brian Pratt responded:  2019-10-10

This will be easiest to investigate if you can provide the Skyline document: use Skyline's File>Share>Complete menu item to create a .sky.zip file, then upload that to http://skyline.ms/files.url and we'll have a look.

Thanks for using the Skyline support board!

Brian Pratt

 
Brendan MacLean responded:  2019-10-10

Also, screenshots of what you are doing and seeing are a great help.