Dear Skyline Users,

The Skyline Team is excited to give you Skyline 20.2, the product of another 8 months of effort in response to your feedback and use of Skyline.

Improvements since Skyline 20.1 include:

• Integrated DDA Search (with MS Amanda) in Import Peptide Search wizard with tutorial
• Support for crosslinked peptides (chemical crosslinking and disulfide bonds)
  • Single-line modified peptide sequence format support for crosslinked peptide targets (supported in Edit > Insert > Peptides)
    • PEPTIDEA-PEPTIDEB-[+mass@a,b]
    • e.g. PETKPESER-EKVLTSSAR-[+138.06808@4,2]
  • Support for loop-links, e.g. AKIQDKEGIPPDQQR-[+138.06808@2-6]
  • Spectral library building support for Proxl XML (http://proxl-ms.org/) of crosslink peptide seaches
• Result File Rules - automated annotation population from result file properties including File Name and File Path
• View > Detection > Replicate Comparison and Histogram plots for applied mProphet models
• Qualitative ion ratio support
• iRT improvements
  • "Automatic" option for iRT standard during library building
  • Non-linear iRT - adding Lowess and Logarithmic regressions
  • Improved iRT handling - especially with CiRT - for File > Import > Assay Library
  • Edit iRT Calculator improvements:
    • Add new IrtStandard using the current calculator's standard peptides
    • Store best transitions and relative ion abundance with calculator
• Made Explicit Retention Time Window limit the range in which peaks are considered.
• Support Thermo SureQuant using Transition Settings > Instrument > Triggered acquisition checkbox
• File > Export > Method support for Bruker timsTOF prm-PASEF methods
• IMS filtering settings moved to Transition Settings - Ion Mobility.
• Added "Protein Results" -> "Protein Abundance" column to reports to expose the protein value used by the Group Comparison framework.
• A new Refine > Advanced - Group Comparison tab making it easy to perform the group comparison refinement demonstrated in Webinar 8 (through Refine > Accept Peptides and a bunch of copy-paste operations)
• Remove based on CV cutoff removes empty peptides
• Refinement based on CV and GC can still remove proteins based on remaining peptide count
• Added Prosit support for Propionamide (C)
• Added a "Product Neutral Loss" column to small molecule transition list reader, which makes it convenient to describe fragments in terms of a chemical formula to be subtracted from the precursor's chemical formula.
• Reduced the number of columns shown by default in the small molecule Insert Transition List grid
• Import Peptide Search Wizard added from and to transition filters and min and max instrument m/z values
• Spectral library building for the DiaNN specLib format.
• Added support for Golm Metabolome Database GCMS spectral library in .MSP format available at http://gmd.mpimp-golm.mpg.de/
• Support even more MSP spectral library format variants for small molecules
• Support for specifying the analyte concentrations for each target by replicate in calibration curves with PeptideResult.ExplicitAnalyteConcentration
• Added apply peak to group
• Added list editing buttons to the Document Settings - Reports tab
• Restored the ability to specify Explicit Collision Energy at the precursor level.
• Decoys checked against targets and warning presented with ability to regenerate if they don't match closely enough.
• Added View > Chromatograms > Close All and keyboard short cuts for Close (Ctrl-F4) and Close All (Ctrl-Shift-F4)
• Removed limit on number of peptides and transitions during File > Import > FASTA - counting on the user to cancel the operation when it is doing more than expected.
• Improved support for MS1-only TIC and BPC
• New resizing progress form to show all status text
• New report values in PrecursorResultsSummary for Detection Q Value (min, max, median)
• Refresh of all links and images for tutorials in the Start Page - Tutorials form
• Some performance improvements for very large DIA documents.
• Command-line not import a raw file from the same path unless a replicate name is specified with --import-replicate-name
• Command-line support for --decoys-discard
• Command-line support for --refine-cv-remove-above-cutoff with decimal percent if value <1
• Improved handling of invalid entries in spectral libraries - warn and filter instead of failing to load
• Many smaller bug fixes such as:
  • Fixed failure to annotate fragment ions in heavy labeled Prosit predicted spectra.
  • Fixed failure to match m/z values between heavy labeled library spectra and Prosit mirror plot spectra.
  • Fixed handling of small molecule .MSP library files without Precursor_type values.
  • Fixed reading LipidBlast .MSP files from MoNA
  • Fixed support for MaxQuant's NotNTerm and NotCTerm fixed mods
  • Fixed bug where MaxQuant spectral library build failing to parse file if it is missing both optional columns "Labeling State" and "Evidence ID".
  • Fixed library build mzML -> MSFragger -> PeptideProphet pipeline (broken by previous fix to TIMS/MGF -> MSFragger -> PeptideProphet; now both pipelines work)
  • Fixed library build file extension detection to be case insensitive.
  • Fixed library build for tilde quotes ("File:~SomeRunName~") in Mascot DAT parser.
  • Fixed library build for ProxlXml parser to not require linker_mass for unlinked peptides.
  • Fixed a problem reading Agilent GCMS SIM SIC chromatograms
  • Increase the threshold scan range at which we consider an MS1 scan to be a "SIM Scan" from 200 to 500
  • Fixed SkylineCmd.exe error reporting when Skyline[-daily].exe are missing and ability to run from downloaded ZIP file without needing to unblock more than SkylineCmd.exe itself.
  • Fixed possible deadlock using SkylineCmd/Runner to import data
  • Fixed calculation of TIC when not MS1-only TIC is available - temporarily reverting to old slower Skyline code to calculate through spectrum summing - faster fix coming
  • Fixed export of negative CoV values for FAIMS methods
  • Fixed IMS display and units in reports to be consistent across PrecursorResults and Chromatogram values
  • Fixed a null reference when dealing with libraries that have inconsistent ion mobility coverage
  • Fixed errors requiring a restart switching iRT standards in the Edit iRT Calculator form
  • Fixed preserving the original standards in an iRT library when standards are changed with the dropdown list
  • Fixed warning about overwriting changes in an iRT library when none have been made
  • Fixed exception using triggered acquisition if some precursors are missing chromatograms.
  • Fixed unhandled error when importing peak boundaries for document with no result files
  • Fixed issues handling SCIEX Midas data
  • Fixed mProphet model training display to avoid empty space on the left and compressed histograms on the right.
  • Fixed "Bandwidth too small" exception doing a Loess regression if there are not enough peptides in the document.
  • Fixed LOQ determination so that it starts looking from the highest concentration point stops looking once it finds a level that fails the criteria.
  • Fixed Shimadzu method numbering
  • Fixed Ctrl-A to work as select all in the Document Grid even when it is docked.
  • Fixed loading Shimadzu SRM files with just 1 chromatogram.
  • Fixed exception bringing up RT Linear Regression window if there are crosslinked peptides in the document.
  • Implemented a workaround for 32 transition limit on Waters method functions.
  • Fixed handling a couple of novel adduct descriptions seen in the wild, e.g. "(M+H)+" and "(M+H)+[-H2O]", which would normally be written as "[M+H]+" and "[M-H2O+H]+" respectively.
  • Fixed NullReferenceException trying to use Triggered Acquisition in small molecule document.
  • Fixed retention time alignment makes mouse act out of phase on aligned replicate chromatogram graphs.
  • Fixed File > Import Assay Library recognizing sequences surrounded by underscores and preceding N-terminal modifications produced by Spectronaut.
  • Fixed pepXML reader looking for pepXML elements inside <analysis_summary>.
  • Upgraded MethodCreator.dll for Agilent method export.
  • Fixed Panorama server checking for in-house Panorama servers.
  • Fixed tooltips on Molecule Settings form for small molecules.
  • Fixed blank IMS spectrum Full-Scan plot when shown in 2D with filtering on.

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