Skyline v3.7 Released on 6/12/2017
New features include:
- Extensive performance improvements in speed and memory use for proteomewide, label-free DIA and DDA data processing
- If you have the hardware, Skyline should be able to use up to 100% CPU and 100% of your memory. Though we continue working on making it do more with less.
- Performance improvements in very large DIA (6,000,000 transitions x 20 files)
- Convergence detection in mProphet modeling and 10 iteration maximum (down from 30)
- New --import-process-count=[num] and --import-theads=[num] arguments for SkylineRunner. The former can yield up to 10x import performance improvement on a 24-core NUMA server and 2-4x on a standard i7.
- Reduced .sky file size by 70% for large (over 1000 transitions) files
- Multi-peptide peak area graph
- Customizable color schemes
- Import isolation scheme feature from DIA data files
- Improved iRT calibration from DDA data directly into spectral libraries
- Storing raw chromatograms in SKYD files. This is a big one which also gives us:
- View > Transform > Interpolated (F12) shows the chromatograms as Skyline used to show them
- View > Transform > None (Shift+F12) shows the raw uninterpolated chromatogram
- Skyline can now always show in Full-Scan graph every spectrum from which chromatograms were extracted. Previously interpolation could cause spectra to be skipped
- A new report value TransitionResults.PointsAcrossPeak
- File > Share can now create document archives in 3.6 format for sharing to Skyline 3.6
- File > Export > Spectral library for exporting targeted results as a spectral library for your next experiment
- Support for semi-cleavage enzymes in Peptide Settings - Digestion tab
- Support for Associate Proteins checkbox in View > Spectral Libraries with background proteome for nonspecific cleavage
- Run-to-run retention time correlation graph
- New file details (score type, score cut-off, unique peptides and spectra) in Spectral Library Explorer source file details form.
- Support BLIB files with StartTime and EndTime in the RetentionTimes table
- Allowing external tools to provide their own peak detection and picking
- Times are used for peak integration boundaries without further peak detection
- Faster imports and smaller resulting files
- File > Import > Peak Boundaries 2-10x faster
- Add Total Ion Current Area under Results.File in reports/Document Grid
- Add "Equalize Medians" as normalization method in Peptide Settings / Quantification for large exploratory experiments where most targets are not changing
- Improved paste performance in the Document Grid
- Column tips and reference help in the Live Report view editor
- New SkylineDailyCmd.exe in same folder as Skyline-daily.exe with same command-line interface as SkylineRunner.exe, but runs Skyline in a single process, useful for ZIP-file or Administrator installations where these EXEs are placed in easily located paths
- Proteome Discoverer 2.2 support in spectral library builder
- Improved support for SCIEX Midas workflow
- Improved support for Agilent IMS workflow
- Improved handling of importing modified peptide sequences with SCIEX 3-letter modification abbreviations
- Export transition list feature for mixed polarity small molecule documents to allow exporting different polarities separately
- Various other fixes such as:
- Use of .NET API to encrypt passwords for Panorama and Chorus stored by Skyline in its user.config file.
- Fix to z ion mass calculation, which was off by one hydrogen atom
- Fix to View > Mass Errors > Replicates graph to match colors with other replicate graphs when MS1 and MS/MS XICs are present
- Fix y axis scaling in chromatograms which had problems when IDs or Predicted annotations were present and scale was less than 100
- Fix tracking of changes to iRT standards to better match changes to documents
- Fix to avoid removing iRT standards when Edit > Refine > Advanced minimum transition count is higher than they contain
- Fix to keep from duplicating spectrum source files - especially problematic for iRT training - in spectral libraries when a DDA file is searched twice
- Slightly more tolerant peak grouping which allows undetected peaks to be added to the group based on chromatogram correlation over the integration boundaries.
- Fix precursor matching with SRM data in fringe case where the precursor m/z is worse, but transition matching is better
- Fix error message reporting missing required columns in File > Import > Peak Boundaries
- Fix to "Unable to sort because the IComparer.Compare() method returns inconsistent results"
Skyline v3.6 Release Updated on 2/21/2017
Skyline v3.6 Released on 11/7/2016
New features include:
- Improved results import:
- Parallel multi-file results import (in user and command-line interfaces)
- New results import interface for improved unattended imports
- Greatly improved import performance for Skyline documents on network drives
- Calibrated quantification improvements:
- Surrogate standards for normalizing to explicit non-homologous molecules
- Remove point right-click option in calibration curve graph
- Explicit Global Standard Area added to replicates for explicit global normalization control with values like TIC
- Group comparison additions and fixes to improve consistency with MSstats
- New Detection Q Value and Detection Z Score report columns for mProphet scored peak picking
- New Peak Rank By Level report value and Targets view showing separate peak rankings for MS1 and MS/MS transitions
- Peptide uniqueness constraint added to Peptide Settings - Digestion tab (by protein, gene or organism)
- New Edit > Refine > Associate Proteins for adding protein associations for targeted peptides after they have been added to the targets list
- Ability to choose which modifictions to use when showing a library in the Spectral Library Explorer
- New and improved plots:
- Mass error plots (replicate and peptide comparisions and 1D and 2D histograms
- Multi-peptide retention time plot
- Point set selection in retention time regression plot
- Improved small molecule support:
- Improved support for negative ion mode
- Improved chromatogram matching for molecules with identical precursor m/z but different scheduled retention times
- Parsing of chemical formula with adduct syntax in Edit > Insert > Transitions
- Support for small molecule transition list import with Edit > Paste, File > Import > Transition List, external tools and with command-line
- Improved Transition Settings for Full-Scan
- Centroided extraction with mass error tolerance made default, based on improvement seen with Thermo, Sciex and Bruker instruments
- New high-selectivity extraction option (1/2 extraction width) for extraction from profile spectra, based on improvement seen with Termo and Sciex raw data files
- Easier import of existing data with improved isolation schemes based on raw data
- Fixed support for importing from instruments using different high- and low-resolution between MS1 and MS/MS
- Ability to include ambiguously matched spectra in spectral libraries build by Skyline
- Improved support for iRT:
- Support for more iRT standard mixes
- Automatic adding of iRT standard targets to document
- More flexible iRT regression support (allowing 80% of standards at 0.995 correlation)
- CiRT support
- SkylineRunner command-line interface improvements:
- Command-line support for importing transition lists and assay libraries
- Command-line support for exporting isolation lists
- Command-line support for adding decoy peptides
- Improvements made to support AutoQC
- mProphet model generation output to console log
- Initial support for Sciex MIDAS data
- Initial support fixes for Waters SONAR data
- Fix for File > Save As bug that disabled Edit > Refine > Re-import
- Many other smaller bug fixes
Skyline v3.5 Release Updated on 1/24/2016
Skyline v3.5 Released on 12/1/2015
New features include:
- Calibrated quantification (a.k.a. absolute quantification) [see tip]
- Impressive performance improvements for large full-scan data sets (DIA and DDA)
- Many longer operations made much faster and showing progress form allowing cancel
- Chromatogram extraction from centroided scans using mass accuracy in PPM (Peptide Settings - Full-Scan tab, using Centroided mass analyzer)
- Improved small molecule support:
- Support for negative polarity ions
- Support for multiple ions per precursor, including isotope labeling
- SkylineRunner command-line improvements supporting processing pipelines from raw data to Panorama uploads
- Improved assay library and transition list import with better modification guessing
- Full support for Panorama AutoQC system suitability run processing
- Support for building spectral libraries from DIA-Umpire search results
- Ability to include report templates in document with Document Settings
- Fill Down function available on Document Grid right-click menu
- Delete-key clears cells in Document Grid
- Apply to All for faster manual correction of multi-replicate peak picking
- Compensation voltage optimization for Sciex instruments with SelexION
- Default Sciex SWATH isolation schemes and abilitly to export Sciex isolation lists
- Automated drift-time training for Agilent and Waters IMS Q-TOF instruments
- Lockmass correction for Waters Q-TOF data
- Export directly to instrument methods for Shimadzu QqQ instruments
- Many display improvements:
- Peak area and background shading of selected transition
- New residuals plot in Retention Times > Regression graph
- Keep ID annotations from being hidden by chromatograms
- Improved dotp display in Peak Areas plot
- Option for strict scientific notation for intensity y-axis on plots
- Graph text scaling based on right-click > Properties for all graph text
Skyline v3.1 Release updated on 4/13/2015
Skyline v3.1 Released on 3/16/2015
New features include:
- Integrated Group Comparison support (see images below). Get started with:
- View > Group Comparisons > Add
- Settings > Document Settings - Group Comparisons tab
- Tutorial coming soon...
- Support for custom ions / small molecule targeted MS
- Use Edit > Insert > Transitions - Small molecules to start a Skyline small molecule document
- Watch Skyline Tutorial Webinar #4 - Preview of Small Molecule Support
- Cloud chromatogram extraction from full-scan data with Chorus
- New wizards for importing peptide searches with PRM and DIA data sets
- Direct filtering of Document Grid views
- Support for iRT scores in chromatogram libraries from Panorama
- Faster start-up and file open and save progress
- Fully enforced light-heavy ion matching and Find form support for "Mismatched transitions"
- Improved optimization library support
Skyline v2.6 Release updated on 2/8/2015
Skyline v2.6 Release updated on 10/27/2014
Skyline v2.6 Released on 9/22/2014
New features include:
- Full-Scan spectrum view for chromatograms extracted from full-scan data, with heat-map graph for IMS data
- New Skyline start page for faster access to common start scenarios and tutorials
- Ion mobility drift time filtering for Agilent and Waters TOF instruments
- Optimization library support for storing optimized CE values
- Custom fragment ion support for defining non-peptide-backbone fragments (like iTRAQ, TMT, etc.)
- Support for isotope labeling experiments (like SILAC) without standards
- Support for Shimadzu triple-quadrupole instruments
- Improved chromatogram peak picking
- Import of tabular "assay library" format
- Support for protein details information (accession number, gene name and preferred name) queried from internet sites
- DIA isolation scheme viewer
- Option to exclude transitions within the DIA isolation window for the precursor
Skyline v2.5 Release updated on 7/10/2014
Skyline v2.5 Release updated on 5/5/2014
With:
- Chinese and Japanese translations
Skyline v2.5 Released on 2/8/2014
New features include:
- Live Reports - interact directly with Skyline documents through a grid interface with
- Customizable column display
- Sort and filter
- Direct paste to annotation values
- Text search
- Much faster report generation than the original Custom Reports
- Improved peak scoring and picking
- Improved default peak picking
- Integrated mProphet scores and semi-supervised learning model training
- Edit > Refine > Reintegrate form for applying non-default peak scoring and picking models
- Peak q value assignment
- Model training and evaluation interface
- Global standard type assignment
- Right-click > Set Standard Type to assign Normalization and QC standard types
- New icons to display iRT, Normalization and QC standard types in Targets view
- New ratio values for peptides, precursors and transitions to global standard types in Peak Areas graph and reports
- All global standard peptides measured in every method of multiple method documents
- Fully integrated Tool Storeuser interface
- Tools > Tool Store form for reviewing and installing External Tools without leaving Skyline or manually downloading files
- Update notifications for new tool releases
- Tools > Updates form for automatic updates to installed tools
- Multi-peptide chromatogram graphs - use protein selection or multiple selection (shift- or ctrl-click) to see annotated chromatogram peaks for many peptides at once
- Improved support for Scheduled Extraction of chromatograms from full-scan mass spectra
- Improved File > Import > Peptide Search wizard
- Thermo raw file import support on systems with European number format settings
Skyline v2.1 Released on 9/8/2013
New features include:
- Support for building chromatogram libraries on Panorama and using them in Skyline
- File > Import > Peptide Search wizard for DDA data quick start
- Mass accuracy metrics for high resolution full-scan data
- TIC and base peak chromatograms from MS1 survey scans
- Installed support for Bruker TOF data, with improved performance
- Demultiplexing of overlapped DIA/SWATH methods
- Improved External Tool integration (see the list of available tools)
- Install from file (Tools > External Tools - click Add button, and choose From File)
- Automatic R installation
- Automatic Python installation
- Support for MSstats with new GUI form [download]
- Support for QuaSAR with new GUI form [download]
- Direct pasting into the Results Grid (especially useful for replicate annotations for external tools)
- Fix to be able to distinguish peptides with the same precursor m/z in MS1 filtered data
- Improved memory performance for large full-scan imports
- Enhanced results data import progress interface with peak graph
- Split chromatogram graphs for simultaneous viewing of light and heavy transitions, and precursor and product ions
- Alignment by iRT scores in graphs
- Improved integration with PanoramaWeb
- Save and restore of Targets View expansion and selection state
- Several spectral library builder fixes, including support for larger libraries and new search pipelines:
- PEAKS pepXML/mzXML
- MSGF+ pepXML/mzXML
- File > Import > Peak Boundaries for importing peak selection from other tools
- File > Export > Chromatograms for exporting chromatogram points
Skyline v1.4 Release Updated on 3/18/2013
With:
- Support for building spectral libraries from Proteome Discoverer MSF
- Support for building spectral libraries from MaxQuant Andromeda msms.txt
Skyline v1.4 Release Updated on 12/17/2012
With:
- Support for building spectral libraries from PRIDE XML
Skyline v1.4 Released on 11/12/2012
New features include:
- Bruker TOF support [details]
- Export triggered MRM (a.k.a. iSRM) transition list support (Agilent and Thermo instruments)
- Peak picking based on retention time alignment of MS/MS IDs for MS1 filtering
- Improved retention time alignment features for MS1 filtering
- Support for publishing Skyline documents to Panorama targeted proteomics repository web sites (server software currently in beta, available early 2013)
- Support for MS1 filtering from SIM scans
- Customizable Tools menu (EXE, Batch and Web site) with macro and custom reports as inputs and command-line customization for installers
- Replicate custom annotations, e.g. Concentration, Case/Control, SubjectId, etc.
(see the updated Existing and Quantitative Experiments tutorial pp. 30-35)
- Replicate comparison graphs grouped by replicate annotations
- Renaming of FASTA sequences (direct edit and Edit > Refine > Rename Proteins)
Skyline v1.3 Release Updated on 8/12/2012
Skyline v1.3 Released on 6/20/2012
New features include:
-
Advanced support for data independent acquisition (DIA) across vendors:
- AB SCIEX SWATH™
- Agilent DIA
- Thermo DIA & Multiplexed DIA
- Waters MSe™
- Isolation list export for Thermo Q Exactive and Agilent TOF instruments
- 64-bit version with higher memory limits
- Retention time alignment for MS1 filtering
- MS/MS retention times in built libraries for more peptide ID pipelines
- Auto-refinement for selecting best responding peptides
- Improved handling for high charge peptides
- Auto-detection of modifications in the Spectral Library Explorer
- Decoy peptide and transition generation for FDR based peak picking
Skyline v1.2 Release Updated on 3/27/2012
Skyline v1.2 Released on 2/15/2012
New features include:
- Integrated display of MS/MS peptide ID spectra in MS1 chromatograms
- Peak picking in MS1 chromatograms based on MS/MS peptide ID retention times
- New isotope dot-product score on MS1 full-scan filtered peaks, and expected relative isotope abundance in peak area plot and reports
- More accurate retention time prediction with integrated iRT Calculator support
- Command-line interface for running Skyline operations in automated scripts on instrument control computers
- Faster MS/MS library loading
- Improved memory performance for full-scan chromatogram extraction
- Improved full-scan method export for Thermo LTQs, including support for Accurate Inclusion Mass Spectrometry (AIMS)
- Full-scan method export for AB SCIEX Q-TOFs, including support for AIMS
- Data import support for Thermo Q-Exactive
- Data import support for Waters Synapt G2-S
- Spectral library build support for iProphet and Protein Prospector pepXML
- New enhanced Find with Find All
- Unexpected error form with button to report the issue
- Manage results, minimize for reducing chromatogram data size in final documents
Skyline v1.1 Release Updated on 8/8/2011
Skyline v1.1 Released on 6/11/2011
New features include:
- Import results from WIFF files much improved (50-fold faster for large scheduled runs - thanks to AB SCIEX)
- Full-scan MS/MS ion chromatogram extraction
- Full-scan MS1 multiple isotope ion chromatogram extraction
- Full-scan method export for Thermo LTQ
- Import document with multiple documents and support for merging results
- Integrated support for Unimod modification definitions
- Modification auto-detect support for pasted/inserted annotated peptide sequences
- Native method export for AB SCIEX QTRAP
- Native method export for Agilent 6400 Series
- Spectral library build support for Scaffold, Waters MS^e and OMSSA
- Improved Edit / Find in the Peptide View
- Larger text sizes in the peptide tree view
- Multi-select annotation editing
- Multiple color annotation indicators
- Improved scheduling for multi-replicate documents
- Variable modification and neutral loss detection in transition list paste/insert/import
- Peptide filter expression support for matching modifications
- New bulk refinement operations
- Replicate acquired time in reports and replicate plot ordering
- New summary plots
Skyline v0.7 Release Updated on 3/30/2011
Skyline v0.7 Release Updated on 2/7/2011
Skyline v0.7 Release Updated on 10/30/2010
Skyline v0.7 Release Updated on 10/5/2010
Skyline v0.7 Released on 9/15/2010
New features include:
- Variable modifications
- Neutral loss product ion transitions
- Native Waters file import support installed
- Spectral Library Explorer
- Multiple heavy label types
- Multi-select copy-paste (text, HTML formatted, and Skyline document to Skyline document)
- Peptide view enhancements (multiple selection, peptide modification highlighting, etc.)
- Spectral libraries built from Protein Pilot results
- Analysis support for fractionation replicates
- Synchronized zooming of multiple chromatogram graphs
- Copy data from graphs to re-plot with your favorite graphing package
- Data import performance improvements for Agilent, AB Sciex and Thermo
- Improved international system settings support
Skyline v0.6 Release Updated on 7/7/2010
Skyline v0.6 Release Updated on 5/21/2010
Now with native WIFF file import support installed.
Skyline v0.6 Release Updated on 4/21/2010
Skyline v0.6 Release Updated on 4/2/2010
Skyline v0.6 Released on 3/17/2010
New features include:
- Improved automatic peak integration
- Collision energy optimization
- Peak area charts
- Peptide summary charts
- Manuscript ready charts
- Results grid with per replicate annotations
- Custom annotations
- Auto-refinement dialog box
- SpectraST library support
- Unique peptides view with a Background Proteome
- Improved support for document sharing
- Summary result statistics in reports
- Waters instrument native method export
Skyline v0.5 Release Updated on 11/8/2009
Skyline v0.5 Released on 9/24/2009
Skyline v0.5 Preview Updated on 8/14/2009
Skyline v0.5 Preview Updated on 7/7/2009
Skyline v0.5 Preview Released on 5/30/2009
The core focus of v0.5 is analysis of result data, building on the successful method creation features of v0.2. Our ASMS 2009 poster gives a broad overview of how we are using these features to extend the scope of our targeted proteomics research at the MacCoss Lab.
New features include:
- Scheduled and unscheduled transition list support for instruments from:
- Agilent
- Applied Biosystems
- Thermo Fisher
- Waters
- Import of results data for instruments from:
- Agilent (native)
- Applied Biosystems (native)
- Thermo Fisher (native)
- Waters (native with MassLynx 4.1 installed)
- All of the above converted to mzML or mzXML
- Share methods and results across labs with different instruments, using Skyline's high-performance, compact data caching
- Build your own spectral libraries from Mascot and X! Tandem search results
- Multiple sample replicates, and multiple replicate import
- Chromatogram plotting with dynamic layout for multi-replicate viewing
- Peak detection and advanced peak picking
- Peak quality indicators
- Isotope labeling ratios
- Advanced peak integration editing
- Dynamic report designer
- Retention time analysis views:
- Linear regression
- Replicate comparison
- Scheduling
Skyline v0.2 Released on 2/17/2009
Skyline is a Windows client application for building Selected Reaction Monitoring (SRM) methods. It aims to employ cutting-edge technologies for creating and iteratively refining SRM methods for large-scale proteomics studies. The latest version of Skyline contains support for:
- Full featured SRM method editing
- Transition list export for Thermo Finnigan TSQ and ABI Q-Trap
- Retention time prediction
- Isotope labeling
- Spectral libraries (NIST, GPM, BiblioSpec)
- Building spectral libraries from your results in TPP pepXML/mzXML
Skyline edits its own universal method format document (saved in XML), and can export transition lists for a variety of instruments. For large, un-refined methods these may be multiple lists per document.
