Skyline
Overview
Skyline [1] is the most popular analysis software for targeted proteomics. It can be used to export spectral libraries suitable for OpenSWATH.
Contact and Support
Skyline is supported by a very active community via their message board.
For TargetedFileConverter, we provide support via the OpenMS support channels.
Tutorial
The Skyline team provides extensive documentation and tutorials and their website. Please follow their instructions to generate spectral or chromatogram libraries. To export a library for use in OpenSWATH, select File and then Report. You can then import the OpenSWATH.skyr report definition file, which will directly export all necessary columns.
Convert the Skyline transition list to a TraML spectral library and follow the remaining steps in the Generic Transition Lists section.