Dear Skyline Users,

After nearly a year of hard work from the entire Skyline team, Skyline 3.6 has just been released. This release again greatly exceeds our previous efforts, and many new people have signed up for the Skyline development release known as Skyline-daily, nearly doubling in number to 1250, and responsible for 25% of all start-ups per week. Along with many thousands of hours of automated test runs, that helps to make this the best-tested Skyline release ever, by far.

New features include:

• Improved results import:
  • Parallel multi-file results import (in user and command-line interfaces)
  • New results import interface for improved unattended imports
  • Greatly improved import performance for Skyline documents on network drives
• Calibrated quantification improvements:
  • Surrogate standards for normalizing to explicit non-homologous molecules
  • Remove point right-click option in calibration curve graph
  • Explicit Global Standard Area added to replicates for explicit global normalization control with values like TIC
• Group comparison additions and fixes to improve consistency with MSstats
• New Detection Q Value and Detection Z Score report columns for mProphet scored peak picking
• New Peak Rank By Level report value and Targets view showing separate peak rankings for MS1 and MS/MS transitions
• Peptide uniqueness constraint added to Peptide Settings - Digestion tab (by protein, gene or organism)
• New Edit > Refine > Associate Proteins for adding protein associations for targeted peptides after they have been added to the targets list
• Ability to choose which modifictions to use when showing a library in the Spectral Library Explorer
• New and improved plots:
  • Mass error plots (replicate and peptide comparisions and 1D and 2D histograms
  • Multi-peptide retention time plot
  • Point set selection in retention time regression plot
• Improved small molecule support:
  • Improved support for negative ion mode
  • Improved chromatogram matching for molecules with identical precursor m/z but different scheduled retention times
  • Parsing of chemical formula with adduct syntax in Edit > Insert > Transitions
  • Support for small molecule transition list import with Edit > Paste, File > Import > Transition List, external tools and with command-line
• Improved Transition Settings for Full-Scan
  • Centroided extraction with mass error tolerance made default, based on improvement seen with Thermo, Sciex and Bruker instruments
  • New high-selectivity extraction option (1/2 extraction width) for extraction from profile spectra, based on improvement seen with Termo and Sciex raw data files
  • Easier import of existing data with improved isolation schemes based on raw data
  • Fixed support for importing from instruments using different high- and low-resolution between MS1 and MS/MS
• Ability to include ambiguously matched spectra in spectral libraries build by Skyline
• Improved support for iRT:
  • Support for more iRT standard mixes
  • Automatic adding of iRT standard targets to document
  • More flexible iRT regression support (allowing 80% of standards at 0.995 correlation)
  • CiRT support
• SkylineRunner command-line interface improvements:
  • Command-line support for importing transition lists and assay libraries
  • Command-line support for exporting isolation lists
  • Command-line support for adding decoy peptides
  • Improvements made to support AutoQC
  • mProphet model generation output to console log
• Initial support for Sciex MIDAS data
• Initial support fixes for Waters SONAR data
• Fix for File > Save As bug that disabled Edit > Refine > Re-import
• Many other smaller bug fixes

Unfortunately, it looks like we still have issues with automatic upgrades between major releases. If you are asked to upgrade automatically after restarting twice, this upgrade will help get you to the installation page to use for upgrading manually. Otherwise, this upgrade will require going to the Skyline download page and installing over your current installation. If this does not work, please consult the Recovering From a Broken Installation page, before requesting support in upgrading.

Enjoy! And thanks again for using Skyline, providing feedback and helping us to continue improving the software.

--Brendan