Dear Skyline Users,

I have just released Skyline 3.7, the product of another 7 months of dedicated effort by the Skyline team in response to your feedback and use of Skyline.

Thanks for a great ASMS and all the inspiring new uses to which you are putting our software. We came home excited and inspired for the next product cycle, with plenty to do.

For now, though, here are the improvements we hope you will enjoy using through the second half of 2017, and we encourage you to join the 1,500 users signed up for Skyline-daily to get early access to the newest features as we add them.

• Extensive performance improvements in speed and memory use for proteomewide, label-free DIA and DDA data processing
  • If you have the hardware, Skyline should be able to use up to 100% CPU and 100% of your memory. Though we continue working on making it do more with less.
  • Performance improvements in very large DIA (6,000,000 transitions x 20 files)
  • Convergence detection in mProphet modeling and 10 iteration maximum (down from 30)
  • New --import-process-count=[num] and --import-theads=[num] arguments for SkylineRunner. The former can yield up to 10x import performance improvement on a 24-core NUMA server and 2-4x on a standard i7.
• Reduced .sky file size by 70% for large (over 1000 transitions) files
• Multi-peptide peak area graph
• Customizable color schemes
• Import isolation scheme feature from DIA data files
• Improved iRT calibration from DDA data directly into spectral libraries
• Storing raw chromatograms in SKYD files. This is a big one which also gives us:
  • View > Transform > Interpolated (F12) shows the chromatograms as Skyline used to show them
  • View > Transform > None (Shift+F12) shows the raw uninterpolated chromatogram
  • Skyline can now always show in Full-Scan graph every spectrum from which chromatograms were extracted. Previously interpolation could cause spectra to be skipped
  • A new report value TransitionResults.PointsAcrossPeak
  • File > Share can now create document archives in 3.6 format for sharing to Skyline 3.6
• File > Export > Spectral library for exporting targeted results as a spectral library for your next experiment
• Support for semi-cleavage enzymes in Peptide Settings - Digestion tab
• Support for Associate Proteins checkbox in View > Spectral Libraries with background proteome for nonspecific cleavage
• Run-to-run retention time correlation graph
• New file details (score type, score cut-off, unique peptides and spectra) in Spectral Library Explorer source file details form.
• Support BLIB files with StartTime and EndTime in the RetentionTimes table
  • Allowing external tools to provide their own peak detection and picking
  • Times are used for peak integration boundaries without further peak detection
  • Faster imports and smaller resulting files
• File > Import > Peak Boundaries 2-10x faster
• Add Total Ion Current Area under Results.File in reports/Document Grid
• Add "Equalize Medians" as normalization method in Peptide Settings / Quantification for large exploratory experiments where most targets are not changing
• Improved paste performance in the Document Grid
• Column tips and reference help in the Live Report view editor
• New SkylineDailyCmd.exe in same folder as Skyline-daily.exe with same command-line interface as SkylineRunner.exe, but runs Skyline in a single process, useful for ZIP-file or Administrator installations where these EXEs are placed in easily located paths
• Proteome Discoverer 2.2 support in spectral library builder
• Improved support for SCIEX Midas workflow
• Improved support for Agilent IMS workflow
• Improved handling of importing modified peptide sequences with SCIEX 3-letter modification abbreviations
• Export transition list feature for mixed polarity small molecule documents to allow exporting different polarities separately
• Various other fixes such as:
  • Use of .NET API to encrypt passwords for Panorama and Chorus stored by Skyline in its user.config file.
  • Fix to z ion mass calculation, which was off by one hydrogen atom
  • Fix to View > Mass Errors > Replicates graph to match colors with other replicate graphs when MS1 and MS/MS XICs are present
  • Fix y axis scaling in chromatograms which had problems when IDs or Predicted annotations were present and scale was less than 100
  • Fix tracking of changes to iRT standards to better match changes to documents
  • Fix to avoid removing iRT standards when Edit > Refine > Advanced minimum transition count is higher than they contain
  • Fix to keep from duplicating spectrum source files - especially problematic for iRT training - in spectral libraries when a DDA file is searched twice
  • Slightly more tolerant peak grouping which allows undetected peaks to be added to the group based on chromatogram correlation over the integration boundaries.
  • Fix precursor matching with SRM data in fringe case where the precursor m/z is worse, but transition matching is better
  • Fix error message reporting missing required columns in File > Import > Peak Boundaries
  • Fix to "Unable to sort because the IComparer.Compare() method returns inconsistent results"

This requires a manual upgrade. We hope you'll take the time to visit the Skyline installation page:

https://skyline.ms/skyline64.url

And install this latest release. It should be worth the effort.

Thanks for your coninued use, feedback and support of this project.

Brendan MacLean
Skyline Principal Developer