Dear Skyline Users,

After many months of hard work from the entire Skyline team, Skyline 3.5 has just been released. There is no question that this release greatly exceeds all of our previous efforts. Word got out, and many new people have signed up for the Skyline development release known as Skyline-daily, now numbering over 750 users, responsible for over 1000 start-ups per week for the past 2 months. Along with hundreds of hours of automated test runs, that helps to make this the best tested Skyline release ever.

With all of the webinars, week-long courses (already 5 scheduled for 2016) and new tutorials, this is also the best documented and supported release of Skyline.

New features include:

• Calibrated quantification (a.k.a. absolute quantification) [see tip]
• Impressive performance improvements for large full-scan data sets (DIA and DDA)
• Many longer operations made much faster and showing progress form allowing cancel
• Chromatogram extraction from centroided scans using mass accuracy in PPM (Peptide Settings - Full-Scan tab, using Centroided mass analyzer)
• Improved small molecule support:
  • Support for negative polarity ions
  • Support for multiple ions per precursor, including isotope labeling
• SkylineRunner command-line improvements supporting processing pipelines from raw data to Panorama uploads
• Improved assay library and transition list import with better modification guessing
• Full support for Panorama AutoQC system suitability run processing
• Support for building spectral libraries from DIA-Umpire search results
• Ability to include report templates in document with Document Settings
• Fill Down function available on Document Grid right-click menu
• Delete-key clears cells in Document Grid
• Apply to All for faster manual correction of multi-replicate peak picking
• Compensation voltage optimization for Sciex instruments with SelexION
• Default Sciex SWATH isolation schemes and abilitly to export Sciex isolation lists
• Automated drift-time training for Agilent and Waters IMS Q-TOF instruments
• Lockmass correction for Waters Q-TOF data
• Export directly to instrument methods for Shimadzu QqQ instruments
• Many display improvements:
  • Peak area and background shading of selected transition
  • New residuals plot in Retention Times > Regression graph
  • Keep ID annotations from being hidden by chromatograms
  • Improved dotp display in Peak Areas plot
  • Option for strict scientific notation for intensity y-axis on plots
  • Graph text scaling based on right-click > Properties for all graph text

Unfortunately, it looks like 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.

You definitely want to make this upgrade, though. This one is worth it.

--Brendan