Dear Skyline Users,

I have just released Skyline 4.2, the product of another 9 months of effort by the Skyline team in response to your feedback and use of Skyline, and the 18th release in 10 years. The first was Skyline 0.1, made to our collaborators at Vanderbilt University who were funding the project as part of NCI-CPTAC.

Here are the improvements we hope you will enjoy using soon and into a productive 2019. We encourage you to join the 2,300 users signed up for Skyline-daily to get early access to the newest features as we add them. Their testing and use accounting for 20% of all start-ups helps us feel confident you will enjoy this upgrade, which includes the following improvements:

• AUDIT LOGGING - yes, really [documentation]
• New Figures of Merit section in Peptide Settings – Quantification tab
  • New LOD and LOQ fields in reports
  • New display in Calibration Curve plot
• New calibration features
  • Regression fit = Linear in Log Space
  • Single-replicate calibration with isotope labeled standards for system suitability
  • Added Sample Dilution Factor field to Replicates in Document Grid for dilution of a sample to bring it within the linear dynamic range
• Support for importing OpenSWATH results through File > Import > Peptide Search - DIA wizard [details]
• Support for using integration boundaries and peak scores from OpenSWATH and EncyclopeDIA
• Drift time predictor training from Use Results fixed for small molecules
• Instrument support improvements:
  • Agilint - support for negative ion mode QqQ data
  • Bruker - timsTOF support for PASEF, All Ions, and PRM
  • SCIEX - support for new SCIEX WIFF2 file format & clearer method export, CE and DP settings
  • Shimadzu - support for 9030 Q-TOF and 8045 QqQ
  • Thermo - support for Thermo FAIMS, GC-MS, Tune v3+ compatibility, and faster raw file reader DLL
  • Waters - advances in SONAR and CCS calibration and importing data from UNIFI server
• Settings > Integrate All no longer affects Precursors.TotalArea nor other quantitative metrics. At last, it is just visual.
• File > Import or Export > Annotations for importing or exporting annotations values directly from or to a CSV file
• New command-line support
  • --import-document = File > Import > Document
  • --import-annotations = File > Import > Annotations
  • --share-zip = File > Share
  • --import-all-files = File > Import > Results of all files in the directory specified, but not subdirectories
  • --import-all[-files] and --import-replicate-name together to import multiple files into a new replicate
  • --reintegrate-exclude-feature = unchecking feature in mProphet model
• New library build support
  • Mascot error tolerant searches and PASEF searches
  • MassIVE mzTab
  • MetaMorpheus mzIdentML
  • Crux Percolator pepXML
  • PEAKS pepXML/mzXML export when scans are out of order
  • Proteome Discoverer ExpectationValue support and pdResult files with multiple workflows
  • MaxQuant deuterium labeling modifications and results lacking Labeling State column
• Added new iRT standard mix RTBEADS
• Added ability to separate CVs in Peak Areas > CV Histogram by precursor or fragment ions in mixed MS1 and MS/MS documents
• Added Plot Type > Residuals to Retention Times > Alignment view
• Faster volcano pot updates and format filtering peptides by protein attributes
• Mouse centered zooming added to some graphs that did not yet have it
• Edit > Delete of transitions removes matching transitions in matching reference precursors
• Edit > Refine > Advanced new option to remove peptides without a matching spectrum
• Added find support for report link columns with text display
• Increased maximum fragment charge state to 20 for whole protein MS/MS
• Increased custom molecule maximum mass from 100 KDa to 160 KDa
• Added a new copy button in the lower-left corner of message boxes to make it clearer that form contents can be copied as text
• Many smaller bug fixes [read more]

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