Dear Skyline Users,

The Skyline Team is excited to give you Skyline 20.1, the product of another 6.5 months of effort in response to your feedback and use of Skyline.

Improvements since Skyline 19.1 include:

• Prosit spectrum and iRT prediction support directly integrated into the UI
  • Building libraries for targeted peptides in a document through Peptide Settings - Library - Build button.
  • Prosit spectrum prediction viewing in the Spectrum Match plot with new right-click menus, including mirror plotting
  • Settings in Tools > Options > Prosit
• Support for spectral library building from MS Fragger pepXML search results
• Support for diaPASEF!
  • We have run this with 2 separate 3-organism datasets through the LFQBench statistical assessment and that works.
• Improved ddaPASEF and initial prmPASEF support.
• Performance gains in importing Agilent and Waters IMS data as much as 2x or more.
• Parallel file import with proteomewide DIA in the UI or by default on the command-line has performance similar to what was previously only available from the command-line using --import-process-count. Choose "Many" on your next import or just ignore threading the next time you import from the command-line.
• Optimized spectrum memory handling for instrument vendors with .NET data reader libraries, benefitting Agilent, SCIEX, and Thermo
• A new "Consistency" tab in the Refine > Advanced form, supporting CV and q value cut-offs
• New checkbox for Refine > Advanced - Results tab Max precursor peak only
• Support for Multiple Attribute Model (MAM) grouping with Peptide.AttributeGroupID and PeptideResults.AttrributeAreaProportion
• Added File.SampleID and .SerialNumber (of the instrument) as fields in Document Grid custom reports
• Transitions Settings - Full-Scan - MS/MS filtering has been extended to apply to all non-MS1 spectra (e.g. MS3) as long as the MS1-level precursor matches the target precursor m/z The redundant library filtering phase of spectral library building is around 20x
• Improved iRT calibration UI making it easy to create new sets of standards based on existing sets that can be used in spectral library building and the Import Peptide Search wizard
• More iRT improvements including more intelligent use of 80+ CiRT peptides when CiRT is chosen during library building
• New right-click > Quantitative menu item for changing the Quantitative property on transitions in the Targets view TIC and BPC now come from raw data files and do not need to be extracted from MS1 spectra which has performance benefits for MS1 filtering
• New global "QC" transitions have been added such as the pressure trace
• Calibration curve fixes to make ImCal (Isotopolog Calibration Curves) work
• New "Calculated" annotations have been added which support storing Skyline calculated values in annotations for future use with AutoQC
• Optional display of spectral library spectrum scores in Spectrum Match, View > Spectral Libraries and in Document Grid
• Added Spectral library building support from "Assay Library" TSV
• New View > User Interface menu item in case the user misses the toolbar button
• New View > Peptides submenu to display modifications in the Targets view text for cases like glycan mods on biologics
• Support for charged losses on peptide modifications like for glycan mods to monitor precursor - lost, minus charge
• New option to order by m/z in exported methods/lists for optimized quadrupole switching Restore the ability to insert a transition list of either type when not in mixed UI mode
• Support KEGG IDs as molecular identifiers in small molecule targets.
• Improved support for D used in chemical formulae in place of the Skyline default H'
• Added support for Thermo Exploris and Eclipse instruments
• Support for opening .skyp files downloaded directly from Panorama
• New command-line arguments:
  • --version - prints the Skyline[-daily] version information to the console
  • --save-settings - saves and settings changes made during the session (e.g. opening a document may add elements to lists)
  • --tran-predict-ce="<name>" - change the Transition Settings - Prediction - Collision energy setting
  • --tran-predict-dp="<name>" - change the Transition Settings - Prediction - Declusering potential setting
  • --tran-predict-cov="<name>" - change the Transition Settings - Prediction - Compensation voltage setting
  • --tran-predict-opt="<name>" - change the Transition Settings - Prediction - Optimization library setting
  • --import-filename-pattern - selects imported files from directory by a pattern
  • --import-samplename-pattern - selects imported samples from a multi-file WIFF by a pattern
  • --ims-library-res command-line argument for adjusting the library IMS extraction resolving power for testing varying settings on 3-organism mixes
  • --share-zip - fixed from being broken in 19.1
  • --exp-order-by-mz - orders transitions in exported methods/lists by m/z for optimized quadrupole switching
• Strong versioning in Skyline-daily.exe and SkylineCmd.exe
  • When you hover the mouse over these EXE files in Windows File Explorer the version number is reported in a tip (no longer just 1.0.0.0)
  • The command-line --version argument now always reports a full version, even for a "developer build" including the Git hash for the source control revision on GitHub, and now the version of ProteoWizard, ensuring the pwiz_data_cli.dll can be loaded.
  • The Skyline Help > About form now also includes this full version with Git hash
• Many smaller bug fixes such as:
  • Spectral libraries from MaxQuant results using spectra from raw data now uses the right spectra
  • Fixed BiblioSpec parser for MaxQuant 1.6.7 mod format
  • Fixed for issue with iProphet and 2H element for MaxQuant
  • Made charge state suffix parsing more flexible to handle the following cases:
    • A series of + or - symbols however long (used to stop at ++++ for positive and -- for negative)
    • Use CultureInfo.TextInfo.ListSeparator (semi-colon in Europe) "; +5" instead of CultureInfo.NumberFormat.NumberGroupSeparator (period, space or apostrophe in Europe) ". +5", " +5", or "' +5"
    • Allow invariant form always ", +5" even when current culture indicates "; +5"
    • Allow the absence of the space in charge states with numbers, i.e. ",+5" or ";+5"
  • Fixed right-click > Order By > Annotation in replicate summary plots
  • Fixed error "Spectrum must have a source file" when doing Import Assay Library tutorial
  • Fixed problem where "batch_name" was not getting written out for replicates.
  • Fixed problem where changing the uniqueness constraint in the Peptide Settings dialog does not result in a new Undo record being created.
  • Fixed error when doing "Export Annotations" if StandardType has been specified for peptides.
  • Fixed error when List has "value list" column type.
  • Exclude peptides from .elib files that do not appear in the "PeptideQuants" table.
  • Fixed missing peak logic when importing with EncyclopeDIA or OpenSWATH results
  • Added support for reading the expect score from Comet pepXML and for using ms2 files for finding spectra of pepXML files.
  • Fixed Tools > Tool Store error message when skyline.ms server is down for maintenance.
  • Fixed controls hidden on Import > Peptide Search form when initiated from the Start page.
  • Fixed problem where Skyline was not acknowledging the isolation windows on MSX scans.
  • Fixed calculation of LOD. It was incorrectly using only using the multiple of the SD of the blank values. It was forgetting to add the mean of the observed values as well.
  • Fixed Precursor Concentration getting blanked out whenever the Peptide Settings changed.
  • Fixed to support a change to the Uniprot interface for querying protein details.
  • Fixed exception when doing "Pick Children" on a small molecule that has two identical precursors.
  • Fixed "Refine > Advanced" max peptide peak rank when there are peptides that only have internal standard precursors and increase maximum peptide peak rank from 10 to 20.
  • Fixed exception that can happen if deselect EmptyNode at bottom of Targets tree while Peak Area Replicate Comparison is shown.
  • Fixed CCS calculation for Bruker data to use 2*N instead of just N.
  • Fixes to improve support for a 1.3 GB Assay Library including a fix to an OutOfMemoryException
  • Fixed progress display of upload to Panorama
  • Fixed Area CV calculation for heavy labeled ratio normalization.
  • Fixed modified peptide sequence text exported from Skyline in .blib spectral libraries to match library builds
  • Fixed unexpected error using Refine > Advanced in small molecule documents with results
  • Fixed renaming a molecule causes miscalculating mass of transition with heavy label adduct
  • Fixed File > Export > Spectral Library losing information from small molecule documents
  • Fixed case sensitivity in library file name extensions

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