Get hands-on experience creating a Skyline document for a targeted proteomics experiment. In this tutorial, you will create a MS/MS spectral library from pepXML and mzXML and a background proteome file from a FASTA format file. You will combine these with a public MS/MS spectral library from the Global Proteome Machine to guide creation of a new Skyline document targeting selected yeast proteins, peptides and product ions. From this document, you will export a transition list, ready to run on a AB 4000 Q Trap. (26 pages)

[pdf] [html] [data]

* - written on Skyline v0.6, updated for v1.4 v2.5, v3.7, v20.1, and v22.2

On February 10th, 2015, the Skyline Team produced Webinar #4: Targeted Method Design with Skyline, another great resource for this foundation topic.
[webinar]