Get hands-on experience starting with a broad set of SRM measurements, importing instrument data, and refining the document. Start with an unrefined document requiring over 2000 transitions and 39 injections to measure unscheduled on a Thermo TSQ. Learn how to import all 39 injections into a single replicate. Use a hydrophobicity to retention time regression and ms/ms spectral library peak intensity correlation to improve confidence in measured peaks. Use the Skyline refinement dialog to remove all but the best transitions for the highest confidence peaks. Step through the scheduling process to reduce the document to a transition list that can be measured in a single injection. Import and view multiple replicates of the single-injection method. (28 pages)

[pdf] [data] [data2]

* - written on Skyline v0.6, updated for v1.4, updated for v3.7, updated for v20.1

Also, see our paper in Proteomics (please cite)
The development of selected reaction monitoring methods for targeted proteomics via empirical refinement
[abstract]

On March 10th, 2015, the Skyline Team produced Webinar #5: Targeted Method Refinement with Skyline, another great resource for this topic.
[webinar]

Learn more about reviewing results and refining your methods by reading the ASMS 2009 poster.