Dear Skyline Users,

The Skyline Team is excited to release Skyline 22.2, the product of another 8 months of effort in response to your feedback and use of Skyline.

Over the past 8 months, you have started 12,500 instances each week (on average) of Skyline or Skyline-daily, and downloaded the software 1100 times per month. There have been 1000 posts to the support board.

Improvements in Skyline 22.2 include:

• New! Protein grouping - through File > Import > Peptide Search and Refine > Associate Proteins.
• New! Library build interface that shows filter cut-offs in a grid, one per file with score type and appropriate scale, i.e. 0.01 for q values.
• Improved DDA MS/MS peak integration to not use background subtraction, proven to work better for producing high dotp values.
• Improved peak picking with DDA acquisition method to use "dotp" score when it is above 0.75, likely from a high-quality MS/MS acquired within or near the MS1 peak.
• Added support for ignoring SIM spectra (commonly used by Thermo as a diagnostic) in MS1 chromatogram extraction.
• Added support for z+1 and z+2 ions for EAD/ETD MS/MS fragmentation.
• Peak Areas plot r/i/dotp line graph support made the default, with customizable cut-off highlighting.
• Added Candidate Peaks view - for new visibility into how Skyline scores and chooses among peaks.
• Added small molecule support to File > Import > Peak Boundaries.
  • Recognizes a "molecule" or "molecule name" column - analogous to the existing "peptide" column for proteomics documents
  • Added a new standard report "Small Molecule Peak Boundaries" for exporting peak boundaries for small molecule documents.
• Added "--import-peak-boundaries" command-line argument.
• Added File > Export > Isolation List support for Bruker timsTOF.
• Added support for redundant iRT databases.
• Added an option to minimize libraries included with a Skyline document uploaded to Panorama.
• Added a context menu option to show collision energy in Full-Scan graph.
• Added method export support for SCIEX 7500.
• Added “natural sort” algorithm to the file explorer and document grid.
• Support for Ion mobility values added for peptide-oriented transition list and assay library imports.
• Improved default peak scoring model training to allow features that have some unknown score values to be used.
• Improved error reporting when importing small molecule transition lists.
• Improved keyboard support for undo (Ctrl-Z) and redo (Ctrl-Y) and fill-down (Ctrl-D) within a floating Document Grid.
• Improved UI of new Edit > Insert > Transition List form with bigger text instruction in the middle of the form.
• Improved error handling for exporting SCIEX method.
• Improved memory consumption in Document Grid when a large amount of Peptide Normalized Area values are being calculated.
• Improved spectrum annotation to allow show/hide of neutral losses.
• Added "[M+]" and "[M-]" to the cascading dropdown control for composing ion formulas in the "Modify..." right-click menu item in the Targets tree for small molecules. These were already available for fragment ions but they are also useful for precursors.
• Added support for heavy copper (Cu' in Skyline formula syntax, Cu65 in adduct syntax)
• Made peptide transition list import "Associate Proteins" option enabled by default when a background proteome is available.
• Fixed the Administrator Installer to avoid causing Windows to show a warning before running it.
• Fixed "Array dimensions exceeded support range" error that can happen when extracting chromatograms from a file with no MS1 spectra.
• Fixed error opening a new Skyline document while there was an uncommitted change in a text box in the Document Grid.
• Fixed unexpected error updating an external tool.
• Fixed reading mzXML from mzML parentFile.
• Fixed mzXML parser to treat invalid scanType attributes (e.g. "CID") as full scan MS1/MSn with a warning.
• Fixed library builder pepXML reader to skip non-AA characters in the unmodified peptide sequence.
• Fixed sticky Y axis in the Full-Scan view.
• Fixed mode-specific (proteomics vs. molecule) reports to show/hide based on the mode and added molecule-specific reports for quantification.
• Fixed some inconsistent handling of attempts to add an empty transition list.
• Fixed a problem with reading transition lists defined by m/z only, and with implied isotope labels.
• Sped up generating the list of peptides with missing values from the edit peak scoring form.
• Fixed chromatogram display when optimization data is asymmetric as when CE values go to zero and below.
• Fixed FASTA parser unexpected error when faced with unusual header lines.
• Fixed NullReferenceException that can happen when extracting chromatograms and predicted retention times are outside of range of spectra.
• Fixed problem where, when doing "File > Share > Minimal", peptides in the document which had modifications would not end up in the minimized iRT database.
• Fixed the display of peak boundaries on the chromatogram graph when all transitions shown are non-quantitative as in DDA.
• Fixed inappropriate use of MS/MS in peak picking scores for DDA acquisition method.
• Fixed unexpected error in Library Match view.
• Fixed unexpected error that can happen showing the PCA plot if the dataset has only one numeric column.
• Fixed unexpected error doing "Apply Peak" when one result file in a replicate was missing results.
• Fixed unexpected error using too long of a path when doing "Save As".
• Fixed Divide by Zero error minimizing a document that has replicates but no chromatograms.
• Fixed error in full scan spectrum viewer that could happen if you rapidly click multiple times on the chromatogram graph.
• Fixed TIC for WIFF files.
• Fixed SkylineDailyRunner.exe to work with Windows user names that contain ampersand (&) or caret (^).
• Fixed synchronized integration behavior when acting on a chromatogram not selected for synchronization.
• Fixed error trying to use small molecule spectral library which did not contain chemical formulas.
• Fixed localization of "Ratio to Global Standards" etc. label on the Y-axis of peak area graph.
• Fixed issues building spectral libraries from Proteome Discoverer files.
• Fixed error that could happen if a particular precursor did not have any results.
• Fixed issue determining score type for .mzid files.
• Fixed error that can happen in small molecule documents if you remove an isotope label type that is still being used by some of the precursors in the document.
• Fixed a problem with Fixed Width ion mobility window value not saving properly when changed in Settings>Transition Settings>Ion Mobility.
• Fixed error displaying multiple peptide chromatogram graph if any of the chosen peaks has a start retention time equal to zero.
• Fixed to not calculate Protein Abundance on the decoy peptide list since it is sometimes very slow.
• Fixed problem with downloading tools that have invalid URL characters in their identifiers.
• Fixed unhandled error when inserting crosslinked peptide sequence which specified "0" as amino acid position.
• Fixed unhandled error inserting crosslinked peptide whose precursor m/z was very close to Instrument Max Mz setting.
• Fixed problem where opening a document with a background proteome and a peptide uniqueness constraint sometimes results in all peptides being removed from document.
• Fixed ion mobility libraries for crosslinked peptides.
• Fixed problem where Skyline would allow transitions which contained multiple crosslink fragment ions which were not actually attached to each other.
• Fixed log scale y-axis label not showing median normalization when appropriate.
• Fixed audit logging in Import Peptide Search wizard when an existing library is used.
• Fixed case where Full-Scan settings impacted peak picking in SRM data.
• Fixed incorrect display of median and TIC normalized values in Peak Area graph.
• Fixed incorrect calculation of median and TIC normalized areas and group comparisons in some replicates.
• Fixed problem where Protein Abundance could not be displayed in a report unless the report also included columns from Peptides.
• Added new document grid columns "Median Peak Area" and "Normalization Divisor" in order to make it easier to see how Skyline calculates normalized areas.
• Fixed calculating of Median Peak Area in the presence of reference standard peptides so that it uses only internal standard label type peak areas.
• Fixed spectrum from incorrect file from EncyclopeDIA library displayed in Library Match window.
• Fixed unhandled error when trying to paste into the Document Grid when it is empty.
• Fixed mass error sometimes reported as zero when "Triggered chromatogram acquisition" was checked.
• Fixed DIA-Umpire on spectra that aren't sorted by m/z (e.g. from scanSumming timsTOF data)
• Fixed a problem with FAIMS on MS2 data in Thermo SureQuant, resulting in jagged chromatograms.
• Fixed support for building spectral libraries from ProxlXML files from Byonic (converted from mzIdentML).
• Fixed unexpected error when exporting Bruker timsTOF methods with ion mobilities outside template range.

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