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 that are not available in any other targeted proteomics software:
  • Open source
  • Freely available and easy to install
  • Vendor-neutral platform for targeted mass spectroscopy investigations of both proteomic and small-molecule data
  • Perform analysis of mass spectrometry data from a range of acquisition techniques such as selected reaction monitoring (SRM), data-dependent acquisition (DDA), parallel reaction monitoring (PRM), and data-independent acquisition (DIA)
    • Support for SRM instruments from Agilent, SCIEX, Shimadzu, Thermo-Scientific, and Waters
    • Support for full-scan instruments from: Agilent, Bruker, SCIEX, Thermo-Scientific and 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 other researchers. 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 Minimize libraries radio button to share only the library spectra used in your document.
    • Click the Store everything radio 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 or methods 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 Settings menu, choose Document Settings, and click the Reports tab.
  • Check the checkboxes beside the names of the reports you wish to share.
  • Save the document.
This will result in the selected reports getting embedded in the .sky XML file. When the file is opened on another computer the reports will automatically get imported making it easy for readers to repeat your analysis on the systems in their labs, with their own samples.

Sharing Skyline results on Panorama Public

Sharing Skyline documents associated with manuscripts is made easier with Panorama Public, a centralized, community resource of published results processed with Skyline. Panorama Public facilitates viewing, sharing, and disseminating results contained in Skyline documents via a web-browser. In addition to viewing results in the Panorama interface, Skyline documents published to Panorama Public can be downloaded in their original form and opened with Skyline for an in-depth exploration.

Submitting Skyline results to Panorama Public involves:
  • Getting a free project for your lab on PanoramaWeb, which is a server repository that is used by several laboratories and organizations to store their Skyline-processed data
    • Click here to request a new project
  • Uploading and organizing Skyline documents within sub-folders of a project on PanoramaWeb
  • Submitting data to Panorama Public
    • Click here for step-by-step documentation
    • Click here for a more detailed tutorial

Data submitted to Panorama Public can be private initially while the manuscript is under review. A reviewer account is provided to the submitter. When the manuscript is accepted for publication data is made public.

Panorama Public is a member of the ProteomeXchange Consortium which is a group of repositories dedicated to the standardized submission and dissemination of proteomics data worldwide. Proteomics data submitted to Panorama Public that fulfills all of the ProteomeXchange requirements is assigned a unique ProteomeXchange accession that can be included in the manuscript. Published data associated with a ProteomeXchange ID is made available to a wider research community via the ProteomeXchange portal and can be searched on the portal with the unique PXD accession number assigned to the data.

Skyline and Panorama Public help you give the proteomics and small molecule research cummunity full, open access to your methods and results.

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