Share Skyline Documents in Manuscripts


Skyline documents provide the ideal way to share targeted proteomics methods and results as supplementary material in your manuscripts.

Skyline has the following advantages available in no other targeted proteomics software:

  • Open source
  • Freely available and easy to install
  • Able to produce transition lists for and import results from the triple quadrupole instruments of
    • AB Sciex
    • Agilent Techonologies
    • Thermo Scientific
    • Waters
  • Human readable XML document format
  • Compact, high-performance, easily shared data cache file format

Once you have created a Skyline document (.sky) and its companion data cache file (.skyd), your entire method and acquired results can be easily shared with the proteomics community.  You are guaranteed that others will have freely available and rich access to your method design and results data.

To create a sharable ZIP file that includes:

  • Skyline document (.sky)
  • Skyline data cache file (.skyd)
  • Skyline display information (.sky.view)
  • Either all used spectral libraries or the fraction used by the document (.blib & .redundant.blib)
  • The backgound proteome file (.protdb - optional)

Simply perform the following steps in Skyline:

  • On the File menu, click Share.
  • If the document uses spectral libraries or a background proteome:
    • Click the Minimal button to share only the library spectra used in your document.
    • Click the Complete button to share the libraries and background proteome files as they exist on your system.
  • Enter the file name of your choice in the File name field (or accept the default).
  • Click the Save button.

You now have a compact file that can be shared publicly or upon request with any manuscript in which your methods and data are included.

Your readers will have open access to:

  • View your methods and data in Skyline's rich visual environment
  • Export transition lists for their own instruments
  • Export custom reports for deeper analysis of your data

You can also share the report template(s) you found most useful in analyzing your data by doing the following:

  • On the File menu, choose Export, and click Report.
  • Click the Share button.
  • Check the checkboxes beside the names of the reports you wish to share.
  • Click the OK button.
  • Enter the file name of your choice in the File name field.
  • Click the Save button.

The resulting Skyline report template file (.skyr) can also be shared with your manuscript along with R scripts to make it easy for readers to repeat your analysis on the systems in their labs, with their own samples.

Skyline helps you give the proteomics cummunity full, open access to your methods and results.