Most of the existing Skyline user documentation can be found in the Videos, Tutorials, Webinars, 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 Custom Reports - Learn about the vast array of values you can show in the Skyline Document Grid or export in tabular format suitable for further analysis in other tools including Excel, R, and Python.
• Skyline Command-Line Interface - Learn about SkylineRunner.exe and SkylineCmd.exe and how you can use them to run certain Skyline operations from a command-line.
• Skyline Keyboard Shortcuts - Learn the keystrokes that give you quick access to your favorite commands in Skyline without ever taking your fingers off the keyboard.
• 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.