Dear Skyline Users,

The Skyline Team is excited to release Skyline 23.1, the product of another 12 months of effort in response to your feedback and use of Skyline.

Since our last release, you have started 13,000 instances each week (on average) of Skyline or Skyline-daily, and downloaded the software 1200 times per month. There have been 1675 posts to the support board.

Improvements in Skyline 23.1 include:

• New! EncyclopeDIA search support in File > Import > Peptide Search for DIA data.
• New! Spectrum filters for extracting separate chromatograms for precursors handled differently in the mass spec e.g. different detectors or fragmentation methods.
• New! Parameter (CE) optimization for TOF and Orbitrap instruments.
• Added spectrum properties to Library Match view.
• Added spectrum properties in the Full-Scan graph.
• Added annotations for "Special Ions" (e.g. TMT) in MS/MS graphs.
• Added library ion match tolerance unit setting in the transition settings to support PPM values.
• Added "ChromatogramStartTime" and "ChromatogramEndTime" to Transition Result Chromatogram in Document Grid.
• Added Skewness, Kurtosis, Standard Deviation, and Shape Similarity Score to Transition Results in Document Grid.
• Added new command-line arguments for building ion mobility libraries: --ionmobility-create-library and --ionmobility-create-library-name
• Bruker PaSER support improvements:
  • Recognize "PrecursorIonMobility" as a synonym for "1/K0".
  • Store ion mobility values from File > Import > Assay library in the .blib file.
• Added library build support for Bruker Paser results and library.
• Added library build support for crosslinked peptide sequences in .ssl files.
• Added library build support for PeptideProphet .proxl.xml files.
• Added library build support for MeroX proxl.xml files and cleavable crosslinks.
• Added support for putting results files in File > Share .sky.zip.
• Added support for showing a library match spectrum with multiple precursors selected.
• Added tooltips on Libraries and Modifications lists in Peptide Settings dialog.
• Added more choices when defining Group Comparisons.
• Added support for Agilent DAD spectra and UIB chromatograms.
• Added log output of the count of BiblioSpec PSMs that do not pass the score filter and improved error message when score filter is the cause of no PSMs being added.
• Added support for File > Export > Method for Thermo Fusion Lumos and Eclipse.
• Added support for File > Export > Method for SCIEX 7600.
• Added pressure trace support for Thermo files.
• Added an error in library builder when SSL peptide sequence has non-uppercase letters or unsupported modification formats.
• Enabled setting the Standard Type of a peptide using "--import-annotations" command line argument
• Added "Skyline 22.2" to the list of available formats in the "File > Share" dialog.
• Added support for Proxl XML files from pLink.
• Added a button to the toolbar in the View > Spectral Libraries form to show extended properties of the spectrum shown in the graph.
• Added a button to the toolbar at top of Report Editor to toggle whether properties are sorted alphabetically.
• Changed the find box on the Document Grid to start out case insensitive.
• Changed right-click > Replicates > Best in the Targets view from being remembered between runs because it can be confusing.
• Improved display display performance of Edit Modifications form.
• Improved support for EncyclopeDIA .elib spectral library files.
• Improved handling of small molecule transition lists where document settings can help with precursor isotopes.
• Improved handling of .skyp files downloaded from Panorama to show progress and request log-in information.
• Improved error handling when downloading MSGF+ fails.
• Improved importing .MSP library files for GCMS use.
• Improved default size of Audit Log, PCA Plot and HeatMap when they are first shown.
• Improved support for interactive tools:
  • Added tool service method "ImportPeakBoundaries".
  • Improved performance of tool service method "DeleteElements".
• Improved error reporting when communicating with Panorama.
• Improved error reporting when unzipping an external tool.
• Improved temp file cleanup and testing when running peptide search tools.
• Improved error handling when parsing FASTA in Associate Proteins form.
• Improved score information on Library Details form in View > Spectral Libraries.
• Improved detection of lockmass function in Waters .raw files.
• Updated to Bruker TDF-SDK v2.21.
  • Added Bruker TSF format support.
• Update WIFF2 SDK to support all instruments.
• Updated handling of Waters DDA data.
• Updated Mascot Parser to 2.8.1 for parsing Mascot DAT files to build spectral libraries.
• Increased limit on number of spectra that could be in a spectral library from 16 million to more than 100 million.
• Fixed View > Transitions > QC showing blank menu item instead of the list of available QC graphs.
• Fixed an unexpected error importing a small molecule transition list lacking anything like a "name" column.
• Fixed library details for EncyclopeDIA .elib files.
• Fixed MSFragger DDA search handle DDA PASEF data correctly.
• Fixed errors caused by assuming lockmass function is not IMS: Invalid Scan Number exceptions.
• Fixed "Order By" menu item disappearing when grouping peak area graph on a replicate annotation which no longer exists.
• Fixed to allow changing score threshold when building library from Waters MSe final_fragment.csv files.
• Fixed bug where half of all transitions in certain .elib files would be marked as non-quantitative.
• Fixed blank panes in peak area peptide comparison when "Transitions > Split Graph" and "Scope > Protein" and selected protein has fewer label types than document.
• Fixed library builder to read MaxQuant msms.txt files with UTF-8 byte order mark.
• Fixed error when crosslinked peptides has heavy atoms.
• Fixed PDF URLs in Start Page to tutorials updated for 22.2.
• Fixed a number of proteomics features still showing up in small molecule UI mode.
• Fixed CCS values to be recalculated as needed in chromatogram extractions for consistency in reports.
• Fixed the Ion Mobility Library Editor to show friendly molecule names in (e.g. "Sulfamethizole" rather than "#$#Sulfamethizole$C9H10N4O2S2$")
• Fixed Ion Mobility Library Editor to avoid absurd high energy offset values from "Find Results"
• Fixed an unexpected error in peptide transition list import.
• Fixed several cases where Skyline could produce a saved file that it could not open.
• Fixed error when crosslinker attaches to invalid amino acid position.
• Fixed calculation of m/z of cleavable crosslink fragments.
• Fixed library build to read ion mobility vendor files in combined spectra form (addresses library build taking forever to try to read MSAmanda searches direct from ddaPASEF .d).
• Fixed to preserve all decimal places of predicted retention times.
• Fixed error doing "Save As" on document with very large .skyd file after removing a replicate.
• Fixed error if SRM chromatogram has zero points in it.
• Fixed hard crash when reading corrupt SQLite file in Bruker data.
• Fixed issue where protein descriptions assigned by "Associate Proteins" would disappear when the document was saved and reloaded.
• Fixed library builder reading newer MSFragger output from timsTOF.
• Fixed MSFragger searches with C-terminal mods giving error "'c' is not an amino acid".
• Fixed a logic flaw where Agilent GC-TOF EI data was mistaken for non-GC all ions data.
• Fixed error clicking on transition with missing chromatogram when viewing single transition chromatogram.
• Fixed converting Shimadzu DDA precursor m/z values from integers; 1e9 instead of 1e5.
• Fixed audit logging for Import Peptide Search to stop logging a global cut-off score when the threshold is specified per file.
• Fixed display of dockable window drop target when dropping near right edge of Skyline window.
• Fixed location of dockable window drop targets when multiple screens have different screen resolution.
• Fixed issue where changes to column values such as "Protein Note" made in the Fold Change grid seemed to disappear immediately.
• Fixed cases where fold change value is NaN if measured peak area is zero.
• Fixed unexpected error right-clicking in Library Match window.
• Fixed unexpected error for protein group metadata during saving.
• Fixed applying Result File Rules when importing results using the command line.
• Fixed Chinese translation of "irank".
• Fixed downloading MSGF+ Java virtual machine.
• Fixed ion type menus in View > Spectral Libraries, Spectrum Match view, and Full-Scan view.
• Fixed an unexpected error that could happen in Import Transition List if .skyd file is modified.
• Fixed the way that the background level under the peak is shaded when TransformChrom is something other than Interpolated.
• Fixed issue where document could not be loaded if a crosslinked peptide was added from the spectral library viewer but the crosslink modification did not have a checkmark next to it in peptide modifications settings.
• Fixed behavior of missing peaks for spectral libraries with peak boundaries (e.g. DIA-NN, EncyclopeDIA, OpenSWATH).
• Fixed error handling in grids appearing in Settings forms.
• Fixed unexpected error on MIDAS library load failure.
• Fixed MIDAS library support in View > Spectral Libraries.
• Fixed unexpected error in spectrum Full-Scan view.
• Fixed handling chemical formulas with zero-count declared atoms.
• Fixed issues with DIA-NN speclib parsing in library builder.
• Fixed Spectral Library Explorer source files view to more consistently report statistics.
• Fixed handling of user editing a molecule in ways that make no sense with child precursor adducts.
• Fixed issue with mirror spectrum between multiple libraries in Library Match view.
• Fixed issue where "--report-add" commandline argument would cause all reports from "External Tools" group to be copied to the "Main" group.
• Fixed chromatogram extraction with ion mobility filtering to use high energy IM offset values for all MS/MS acquisition modes rather than only "All Ions".
• Fixed issue where Library Match graph disappears if spectrum being displayed has no intensities that are greater than zero.
• Fixed unexpected error using Prosit when precursor charge was greater than 6.
• Fixed assay library importing to handle unsorted transition lists.
• Fixed toolbar buttons and right-click menu in View > Spetral Libraries broken adding property page.
• Fixed very large (e.g. 6 million lines) Assay Library import.
  • Fixed out-of-memory error.
  • Fixed performance bottleneck introduced in checking for lines with irregulate column counts before starting to import.
  • Fixed requiring large recalculation when "Check For Errors" was already clicked.
• Fixed "The document specific spectral library does not have valid retention times" when importing peptide search existing EncyclopeDIA 2.0 library.
• Fixed a problem with Agilent IMS data where fringe CCS and/or DT values cannot roundtrip through the CCS/DT conversion.
• Fixed a case where saving document after removing modification with neutral losses from settings results in a document which cannot be opened.
• Fixed a case where ion mobility library entries for crosslinked peptides would be duplicated each time you pressed the "Use Results" button .
• Fixed peptide losses with multiple charge states not all appearing in the transition options.
• Fixed peptide charged losses changing to small molecule adducts line [M+H].
• Fixed Result File Rule Set Editor to allow using newly added annotations without having to first OK the Document Settings dialog.
• Fixed Document Grid (and other data grids) so that custom formats are applied when doing "Copy All" or "Export".
• Fixed unexpected error changing annotation value in document grid when the document had been changed.
• Fixed issue where removing an explicit modification from a document with decoys could result in a document that could no longer be opened.
• Fixed exporting Waters methods containing compounds with multiple modifications and more than 5 transitions.
• Fixed behavior where graphs would appear blank if the Legend took up all of the space in the graph.
• Fixed several issues with Bruker data:
  • Fixed timsTOF instrument type not being recorded in instrumentConfiguration.
  • Fixed negative CE in negative polarity Bruker data not being reported.

This release will 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