Skyline

Skyline

Release Notes

 

Skyline v4.1 Release Updated on 2/18/2018

Skyline v4.1 Released on 1/11/2018

  • Improved small molecule support [detail slides]
    • Support for NIST and self-built (from SSL format) small molecule spectral libraries with fragment annotation
    • Neutral molecules with multiple precursor adducts
    • Improved support for pasting small molecule transition lists with column headers
  • Bruker TIMS support that parallels IMS support for other vendors
  • A new Document Grid pivot editor and saved report layouts [detail slides]
  • Improved Import Peptide Search wizard for DIA with DDA for the mProphet workflow
  • File > Import > Assay Library makes importing Assay Library files easier than File > Import > Transition List
  • More performance improvements (memory use and speed) for large-scale DIA data processing
  • Interactive volcano plots for group comparisons with custom formatting [detail slides]
  • Interactive peak area CV histogram plots [detail slides]
  • High precision modification delta-mass support past a single decimal place
  • Points across the peak and manual integration adjustment visualizations in chromatogram plots [detail slide]
  • New line plot modes for summary (Replicate and Peptide Comparison) plots
  • Synchronized zooming available in summary (Replicate and Peptide Comparison) plots
  • New Import Results common prefix and suffix removal UI with real-time replicate name display
  • New delete button (red X) on the Document Grid
    • allows deletion from the Targets View (proteins, peptides, precursors and transitions)
    • filter and delete.
  • Possible to rename replicates from Document Grid (including copy-paste) with "Replicate Name" field
  • New "Exclude From Calibration" column on PeptideResult
  • New Quantitative column on Transitions [detail slides]
  • New non-blocking background population of Document Grid with full support for chromatogram values (times, intensities, mass errors) in Live Reports, both interpolated and raw values
  • New Edit > Integration menu with shortcuts for Remove Peak and Apply Peak to All
  • Display an informative warning when iRT calibration fails during import
  • Improvements for library building from peptide search formats which do not support probability cutoffs to make sure they get ordered correctly
  • Many other fixes...

Skyline v3.7 Release Updated on 9/10/2017

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.