Learn how how to create a Skyline document that targets stable isotope labeled small molecules from a literature citation, specified as only precursor m/z, product ion m/z, and collision energy values. Perform retention time scheduling and collision energy optimization for small molecules by importing a multi-replicate data set from a Waters Xevo TQ-S using initial CE values from a Sciex triple quad. Learn how many existing Skyline features created initially for targeted proteomics use can now be applied to small molecule data. (37 pages)

[pdf] [html] [data]

* - Originally written for Skyline 4.1, updated for 19.1, 20.1, and 23.1

On February 10th, 2015, the Skyline Team produced Webinar #4: Targeted Method Editing with Skyline, with a sneak peak of small molecule support.
[webinar]

On November 7th, 2017, the Skyline Team produced Webinar #16: Small Molecule Research with Skyline, with new material on small molecule support.
[webinar]

Learn more about using Skyline for small molecule quantification by reading this MSACL 2015 poster.