Generating optimization method for small molecules

Generating optimization method for small molecules William  2022-03-28

I generated a optimization method (small molecule) for Shimadzu QQQ. I remember that Skyline recognize different CEs by varying the product ion in one digital difference. However, when I open the method I find that product ions for different CEs are all the same. How can Skyline recognize different CEs?

Nick Shulman responded:  2022-03-28
When you export a Shimadzu method, the product m/z's all end up being identical.

As you mentioned, with all the other machine types, Skyline changes the product m/z by 0.01 to indicate that this is a group of CE optimizing chromatograms.

When you import results from a Shimadzu file, Skyline notices that there are multiple chromatograms with the same Q1 and Q3 values, and Skyline also notices that the CE values have a constant interval in them (for Shimadzu data, Skyline is able to read the CE values), and so when the chromatograms get put into the .skyd file, they end up looking just like optimization chromatograms from any other vendor, and everything will look right in Skyline.
-- Nick