Dear Skyline Users,

The Skyline Team is excited to release Skyline 21.2, the product of another 7 months of effort in response to your feedback and use of Skyline.

Over the past 7 months, you have started 11,000 instances each week (on average) of Skyline or Skyline-daily, and downloaded the software 1450 times per month. There have been 1100 posts to the support board.

Improvements in Skyline 21.2 include:

• New! Synchronized Integration (right-click in a chromatogram graph)</li>
• New! Improved SureQuant support with "SureQuant" MS/MS acquisition method and method export for Exploris.
  • Also added new PRM acquisition method (an improvement over the old "Targeted" method – now deprecated).
• New! Added support for DDA searches with MS Fragger and MSGF+, now options in the Import Peptide Search wizard.
  • See the DDA Search tutorial for more information on integrated DDA searches in Skyline.
• Prompt to create decoys for DIA data and when decoys are present auto-train a default model to add q values and z scores.
• Improved memory use for large-scale DIA to use less than half the memory in most cases.
• Improved DIA-Umpire performance in Skyline.
• Added support for transition list import with column selection form for small molecules.
• Improved transition list column selection form to support Associate Proteins.
• Replaced Edit > Insert > Transition List with for pasting text followed by the transition list column selection form to be consistent with direct pasting and File > Import Transition List.
• Line graph representation of dotp/idotp/rdotp in the Peak Areas > Replicate Comparison plot - using right-click menu.
• Changed rdotp calculation to be consistent with dotp and idotp - using spectrum contrast angle.
  • This will tend to reduce rdotp values slightly if comparing rdotp values after this change with those before it.
• Added RT annotation display digits on the chromatogram graph right-click > Properties form.
• Improve library building error message for unrecognized modifications in PLGS outputs to include the ones we will recognize.
• Improved layout of Import Peptide Search wizard forms when ion mobility values are present, e.g. diaPASEF
• Improved Export > Spectral Library to use best score instead of first and include z-score.
• Improved library building support for MSFragger.
• Improved performance importing large .MSP spectral library files.
• Added ability to switch between centroided and profile spectra in Full-Scan view.
• Added mass error annotation display to Full-Scan and Spectrum Match views.
• Added rdotp annotation in Peak Areas > Replicate Comparison view when showing ratios.
• Added new filter categories to the Spectral Library Explorer, especially helpful for small molecules.
• Added support for reading from vendor formats when library build searches for spectra for pepXML ids.
• Switched to using peptide level q values in pdResult files and special handling for 1% and 5% FDR cutoffs to be more consistent with Spectronaut library builds.
• Added support for previously unseen "VIP_HESI" ion source in Bruker TIMS data.
• Added support for the latest chromatogram library export from Panorama, including new support for ion mobility and small molecules.
• Improved menu options for MS/MS annotations in the Full-Scan view.
• Skyline no longer requires .NET 3.5.
• Only write top-ranked transitions when exporting any CoV optimization method
• Added a warning when exporting a prmPASEF method for timsTOF with wrong CE setting.
• Export polarity column for Thermo Fusion when Tune v3 is checked.
• Enabled writing CoV values for Thermo Fusion.
• Improved support for Waters SONAR data.
• Updated SCIEX interop DLLs for method export.
• Update Shimadzu DLLs for method export.
• Added support for Agilent/Mobilion SLIM data.
• Added LC/QC chromatograms for Agilent data.
• Added tooltips on feature names in mProphet model form.
• Fixed peak scoring for documents using DDA acquisition method in Transition Settings - Full-Scan tab for MS/MS filtering.
• Fixed Skyline to report AA positions in proteins starting at 1 instead of zero.
  • Added the columns "First Position" and "Last Position" to the document grid which show the 1-based amino acid position of the peptide in the protein.
  • Changed the numbers that are displayed in the Targets tree so that they are 1-based instead of 0-based.
  • Columns "Begin Pos" and "End Pos" are now marked "Obsolete", which means that they only show up in the Report Editor if you push the "show all columns" button.
• Fixed problem where peaks with integration boundaries that were chosen by the user did not get their areas recalculated when you do a reimport.
• Fixed handling all-ions DIA for Bruker timsTOF bbCID.
• Fixed a problem reading Bruker files with multiple TIMS calibrations.
• Fixed library building from DIA-NN speclib to support version 3, and added support for reading scores and ion mobilities.
• Fixed peptide-specific settings showing up in the Transition Settings - Library tab when in small molecule mode.
• Fixed MSAmanda running on DDA WIFF files.
• Fixed handling unexpected errors during auto-training of an mProphet model.
• Fixed case where "Ratio To" menu item in Targets view did not agree with "Normalize To" in Peak Areas view.
• Fixed problem removing a Prosit library for library matching in Molecule UI.
• Fixed unexpected error in heat map graph during a selection change.
• Fixed Agilent method export for scheduled methods
• Fixed an issue where a mass-only transition list import of a labeled precursor would come up with the unlabeled mass for the precursor transition.
• Fixed "Missing transition precursors when you do Refine > Permute Isotope Labels".
• Fixed "Item with the same key already added" when two small molecules have no Name, same precursor m/z and different set of transitions.
• Fixed an unexpected error when attempting to parse an ill-formed adduct description.
• Fixed InvalidOperationException choosing "Transform > None" when the displayed chromatogram has optimization steps.
• Fixed loading libraries from read-only drive location.
• Fixed problem where blank document created from the Start Page sometimes never loads.
• Fixed unexpected error in Import Peptide Search when importing multiple results files with the same name.
• Fixed preserving scores when using File > Export > Spectral Library.
• Fixed command-line documentation to use <nobr> tags instead of non-breaking hyphen for easier copy-paste.
• Fixed transition list logic to decide proteomic vs. small molecule based on UI mode when no other indicators work.
• Fixed right-click > Copy in any graph to show a useful error message if the clipboard is locked by another application.
• Fixed error that happens if you set Instrument Min Time, but leave Instrument Max Time blank.
• Fixed a problem where if "Triggered Acquisition" was chosen on Transition Instrument Settings, the reported peak areas would all be 60 times smaller than they should be (but did not impact light:heavy ratios).
• Fixed Spectral Library Explorer handling of peptide with modified 'X'.
• Fixed a problem where "Protein Abundance" column would display as "column not found" if the report also had any peptide-level columns.
• Fixed tolerance of Shimadzu .lcd files not containing TIC information.
• Fixed how Skyline detects the difference between peptide and small molecule transition lists to be first based on finding a peptide sequence with a matching precursor m/z.
• Fixed writing CE and DP to large Skyline documents for upload to Panorama.
• Fixed coloring of peak annotations in MS/MS spectra for small molecules.
• Fixed filtering of targets when building spectral libraries from existing BLIB files.
• Fixed an infrequent potential race condition in the DIA-Umpire implementation.
• Fixed transition list column picker saving column assignments only when they are valid.
• Fixed a recently introduced problem where we were not identifying transition list columns as numeric if the values were in quotes.
• Fixed MaxQuant spectral library build to check up to 4 levels above msms.txt for spectrum files and improved the error message when files are not found.
• Fixed a problem processing Waters Cyclic IMS data, wherein the lockmass functions do not have IMS data.
• Fixed order by m/z method export bug when multiple precursors have the same m/z.
• Fixed cases where "View" was used in the UI instead of "Reports".
• Fixed calculation of R-squared for calibration curves that use "Linear in Log Space" fit.
• Fixed an unexpected error that can occur when "Transition Settings > Ion Mobility > Use spectral library values when present" is enabled.
• Fixed View > Library Match y-axis was not updating correctly in response to changes in selection in the Targets view.
• Fixed .skyd file corruption problem which could happen if there were more than 60 million candidate peaks.

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