Most of the existing Skyline user documentation can be found in the Videos, Tutorials and Tips sections. Here, however, are a few documents which do not fit into those categories, but still provide useful information on advanced topics in using Skyline for targeted proteomics data analysis:
Skyline Command-Line Interface - Learn about SkylineRunner.exe and how you can use it to run certain Skyline operations from a command-line.
NOTE: for the most current command-line documentation, run SkylineRunner.exe or SkylineCmd.exe without any command-line arguments. The same information can be found in the Skyline user interface at Help > Documentation > Command Line.
Skyline External Tools Documentation - Learn how to integrate with Skyline statistical and bioinformatics tools you are developing.
Skyline Interactive Tools Documentation - Learn how to integrate with Skyline interactive tools written with .NET which can request data from Skyline and respond to document changes on the fly.