Dear Skyline Users:

Only 5 months after releasing v2.1, I am extremely excited to announce the release of Skyline v2.5. As the numbering indicates, this is a big jump for such a short release cycle. This is because we are releasing advances in two major areas that have been under development, but not yet released, for over a year:

• Live Reports
• mProphet/OpenSWATH integration

We haven't stopped working on these areas, but you will be seeing years of development time in this release. The full feature set added in v2.5 includes:

• Live Reports - interact directly with Skyline documents through a grid interface with
• Customizable column display
• Sort and filter
• Direct paste to annotation values
• Text search
• Much faster report generation than the original Custom Reports
• Improved peak scoring and picking
• Improved default peak picking
• Integrated mProphet and OpenSWATH scores and semi-supervised learning model training
• Edit > Refine > Reintegrate form for applying non-default peak scoring and picking models
• Peak q value assignment
• Model training and evaluation interface
• Global standard type assignment
• Right-click > Set Standard Type to assign Normalization and QC standard types
• New icons to display iRT, Normalization and QC standard types in Targets view
• New ratio values for peptides, precursors and transitions to global standard types in Peak Areas graph and reports
• All global standard peptides measured in every method of multiple method documents
• Fully integrated Tool Store user interface
• Tools > Tool Store form for reviewing and installing External Tools without leaving Skyline or manually downloading files
• Update notifications for new tool releases
• Tools > Updates form for automatic updates to installed tools
• Multi-peptide chromatogram graphs - use protein selection or multiple selection (shift- or ctrl-click) to see annotated chromatogram peaks for many peptides at once
• Improved support for Scheduled Extraction of chromatograms from full-scan mass spectra
• Improved File > Import > Peptide Search wizard
• Thermo raw file import support on systems with European number format settings

To help you get up to speed on these latest advances, we have written a new peak picking tutorial and majorly revised three other tutorials (MS1 Full-Scan Filtering, Targeted MS/MS, Custom and Live Reports), which you can find here:

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

If you are using a recent public release (i.e. v2.1 or v1.4), 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. I look forward to meeting many more of you this year at the courses and conferences where Skyline and targeted proteomics will be taught and discussed.

Brendan MacLean
Skyline Project Lead