Dear Skyline Users:

After nearly 10 months of hard work by a growing and vibrant team of software developers and scientific collaborators, with a lot of great feedback from many of you, I am proud to announce that Skyline v2.1 has been released.

Two of the most exciting developments in the past year have been integrating new supporting tools around Skyline:

• Panorama Targeted Proteomics Knowledge Base - a data base web site for sharing, storing and reviewing collections of Skyline documents, and for creating Chromatogram Libraries from empirically measured targeted data.
• External Tools - a new collection of external statistical tools directly integrated into Skyline with automated installation support, including MSstats for grouped studies and QuaSAR for response curves, LOD/LOQ and AuDIT interference analysis, and hopefully many more to come.  Download the ZIP files and follow the tutorials to get started.

Other new features include:

• File > Import > Peptide Search wizard for DDA data quick start
• Mass accuracy metrics for high resolution full-scan data
• TIC and base peak chromatograms from MS1 survey scans
• Installed support for Bruker TOF data, with improved performance
• Demultiplexing of overlapped DIA/SWATH methods
• Direct pasting into the Results Grid (especially useful for replicate annotations for external tools)
• Fix to be able to distinguish peptides with the same precursor m/z in MS1 filtered data
• Improved memory performance for large full-scan imports
• Enhanced results data import progress interface with peak graph
• Split chromatogram graphs for simultaneous viewing of light and heavy transitions, and precursor and product ions
• Alignment by iRT scores in graphs
• Improved integration with PanoramaWeb
• Save and restore of Targets View expansion and selection state
• Several spectral library builder fixes, including support for larger libraries and pepXML/mzXML from PEAKS
• File > Import > Peak Boundaries for importing peak selection from other tools
• File > Export > Chromatograms for exporting chromatogram points
• Bug fixes too numerous to count

If you are using a recent public release (e.g. v1.4 or v1.3), then Skyline should ask you to upgrade automatically after you restart twice.  If it does not, please consult the following web page before you post a support request:

https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tip_recover_install

Thanks for using Skyline in your research.  This really would not be possible without all of you.

Brendan MacLean
Skyline Project Lead