Dear Skyline Users,

I have just released Skyline 19.1, the product of another 8 months of effort by the Skyline team in response to your feedback and use of Skyline. This is the 19th official release and the first of 2019. So, for this 10th anniversary realese, we are changing to a year-based version number like many other mature products.

Improvements since Skyline 4.2 include:

• New! Small molecule and proteomics UI modes [introduction]
  • And a form that asks for your preferred mode once
• iRT and Optimization library support for small molecules
• New! Lists - define lists of values in multiple columns and associate them with elements in your documents through annotations.
  • See Document Settings – Lists
• Batch calibration
• Import > Peptide Search with an existing library (including EncyclopeDIA .elib files)
• A new MS/MS filtering Acquisition method named "DDA" which sets all fragment ions to non-quantitative and does not truncate MS1 chromatograms the way "Targeted" (or PRM) does.
• Edit > Refine became a top-level Refine menu between Edit and View and got reorganized for ease-of-use.
• The Document Grid "Views" menu has been changed to "Reports" to better align with File > Export > Report and Document Settings - Reports
• Added Actions menu to the Document Grid to enable bulk peak removal based on filtering
• New command-line help for SkylineRunner/SkylineCmd available with --help argument and Help > Documentation > Command Line in Skyline
• Command-line support for Refine > Advanced options
• Command-line support for setting precursor charge states, fragment charge states and fragment types
• Moved some explicit parameter values like CE from precursor to transition level
• Audit log improvements to support working with Panorama and tampering detection
• Building a library from MaxQuant msms.txt now attempts to find the original spectrum source files and use the spectra in them to avoid using charge state deconvoluted spectra, but allows the user to override this default if the spectrum source files cannot be found
• A new <Edit current...> choice in the dropdown lists in Edit > Modify Peptide to make updating specified modification definitions easier
• Improved handling of common background proteome building problem where user tries to open or create the FASTA file causing it to be overwritten by an empty PROTDB file
• Changed File > Share default to "Complete" instead of "Minimal"
• Add "PeptideResult.ModifiedAreaProportion" which is the normalized area of the PeptideResult, divided by the sum of the other NormalizedAreas for all of the other PeptideResults in the same replicate and protein that have the same unmodified sequenceAdded new Transition.LossFormulas field
• Allow grouping by built-in properties such as "concentration" in addition to annotations in peak area graph
• Many smaller bug fixes such as:
  • Fixed to support C-terminal modifications in MaxQuant msms.txt
  • Fixed library building for PeptideShaker results
  • Fixed to add the .wiff2 extension to File > Import > Results form
  • Fixed to support File > Export > Method for Thermo Altis
  • Fixed to allow package installation for R external tools (like MSstats) in China
  • Fixed for calibration curve text exported to report CSV files on Chinese and Japanese systems
  • Fixed library building from paths with extended characters
  • Fixed for spectral library building of Peaks mzIdentML/MGF export
  • Fixed library building support for ProXL cross-linked peptides with PTMs
  • Added support for radioactive 14C labeling as C"
  • Added support for deuterium as D and H' and tritium as T and H"
  • All elements in the periodic table now allowed in chemical formulae
  • Fixed for q value cut-off advanced option in group comparison definition form
  • Fixed to apply chromatogram transformation to non-quantitative chromatograms to match quantitative chromatograms
  • Fixed for invalid precursor transitions after changing Full-Scan settings
  • Performance improvement for importing large small molecule transition lists
  • Fixed to Support new variant of retention time specification in NIST .msp library format
  • Fixed audit log saving to use write and rename to avoid log truncation
  • Fixed audit log enabling to create undo records and be more persistent
  • Fixed to handling of invalid adduct specification
  • Fixed to small molecule persistence with multiple keys
  • Fixed undo/redo of setting standard type
  • Fixed problem where modifications with negative mass cannot be found in iRT database (reported by Anatoly, thanks to Nick)
  • Updated UIMFLibrary DLLs to version 3.6.6
  • Fixed library build support for reading MaxQuant fixed peptide-N/C-terminal modifications
  • Fixed parsing of pS/pT/pY variant of phospho mods from MaxQuant
  • Fixed issue parsing PLGS final_fragment.csv modifications with paren’s in the mod name
  • Fixed problem with implicit modifications not being included in "Modified Sequence" column in Document Grid
  • Fixed importing report layouts from a .skyr file
  • Fixed reading Shimadzu QTOF files that also open with the QQQ reader DLL
  • Change SCIEX centroiding to multiply Y (area) values by 100 to make the numbers more similar to profile extraction (requested by SCIEX)
  • Fixed Area CV histograms to ignore precursors with no chromatograms rather than Calculating... forever
  • Fixed to continue importing chromatograms when iRT regression fails as long as chromatogram extraction is not dependent on it

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