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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 :doc:`generic` section.

References

[1]MacLean B, Tomazela DM, Shulman N, Chambers M, Finney GL, Frewen B, Kern R, Tabb DL, Liebler DC, MacCoss MJ. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics. 2010 Apr 1;26(7):966-8. doi: 10.1093/bioinformatics/btq054. Epub 2010 Feb 9. PMID: 20147306