Dear Skyline Users,

I have just released Skyline 4.1, the product of another 7 months of dedicated effort by the Skyline team in response to your feedback and use of Skyline.

Here are the improvements we hope you will enjoy using through the first half of 2018, and we encourage you to join the 1,800 users signed up for Skyline-daily to get early access to the newest features as we add them. Their testing helps us feel confident you will enjoy this upgrade.

• Improved small molecule support [detail slides]
  • Support for NIST and self-built (from SSL format) small molecule spectral libraries with fragment annotation
  • Neutral molecules with multiple precursor adducts
  • Improved support for pasting small molecule transition lists with column headers
• Bruker TIMS support that parallels IMS support for other vendors
• A new Document Grid pivot editor and saved report layouts [detail slides]
• Improved Import Peptide Search wizard for DIA with DDA for the mProphet workflow
• File > Import > Assay Library makes importing Assay Library files easier than File > Import > Transition List
• More performance improvements (memory use and speed) for large-scale DIA data processing
• Interactive volcano plots for group comparisons with custom formatting [detail slides]
• Interactive peak area CV histogram plots [detail slides]
• High precision modification delta-mass support past a single decimal place
• Points across the peak and manual integration adjustment visualizations in chromatogram plots [detail slide]
• New line plot modes for summary (Replicate and Peptide Comparison) plots
• Synchronized zooming available in summary (Replicate and Peptide Comparison) plots
• New Import Results common prefix and suffix removal UI with real-time replicate name display
• New delete button (red X) on the Document Grid
  • allows deletion from the Targets View (proteins, peptides, precursors and transitions)
  • filter and delete.
• Possible to rename replicates from Document Grid (including copy-paste) with "Replicate Name" field
• New "Exclude From Calibration" column on PeptideResult
• New Quantitative column on Transitions [detail slides]
• New non-blocking background population of Document Grid with full support for chromatogram values (times, intensities, mass errors) in Live Reports, both interpolated and raw values
• New Edit > Integration menu with shortcuts for Remove Peak and Apply Peak to All
• Display an informative warning when iRT calibration fails during import
• Improvements for library building from peptide search formats which do not support probability cutoffs to make sure they get ordered correctly
• Many other fixes...

This release may require 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 continued use, feedback and support of the Skyline Project.

Brendan MacLean
Skyline Principal Developer