CE optimization on a Sciex Qtrap alejandro.cohen  2021-07-15
 

Hi Skyline people

We are performing a CE optimization on a SMR experiment run on a QTrap5500 for small molecules, and following the Tutorials. Experimentally, everything worked fin.
We exported the Transition list into the .dam files with multiple the CEs, and reacquired data on known standards. When reimporting the wiff files into Skyline, we get the expected 'curve' for the CEs.

The Replicate graphs show a legend for the colors and CE Steps (-10,-9. etc).

Is there a way for Skyline to show the nominal CEs used by the instrument in the graphs instead of the Steps? Or, is there any parameter in the Document grid to show the Nominal CEs??? All the parameters with CEs I select show either calculated values, or Steps.

Hope I made myself clear!

Cheers

Alejandro

 
 
Brendan MacLean responded:  2021-07-28

The relevant Document Grid fields are:

Precursors.Collision Energy - the predicted optimal collision energy
PrecursorResults.Opt Collision Energy - prediction + step * step size (or #N/A for step = 0 when it is the above value)
PrecursorResults.Opt Step

I am not sure I am fan of Opt Collision Energy showing #N/A instead of just passing through Collision Energy when step = 0.

Is this at all helpful? The request to show these values in the graphs came up during development. I can't remember why it wasn't done. Maybe something to do with why the values are on PrecursorResults? In theory, the step could have different meanings across different runs. Certainly, you could have 3 runs imported that each optimizes one of CE, DP, and CoV. I get that this is not a very likely case, but the meaning of the step is assigned during import when you tell Skyline what you were optimizing with the run.

Thanks for posting to the Skyline support board.

--Brendan