Skyline vNext Development Under Way

Get these features in Skyline-daily now! [here]

• Improved small molecule support
  • Support for NIST and self-built small molecule spectral libraries
  • Neutral molecules with multiple precursor adducts
• Imporved 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
• Interactive peak area CV histogram plots
• Points across the peak and manual integration adjustment visualizations in chromatogram plots
• Synchronized zooming available in summary (Replicate and Peptide Comparison) plots
• 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
• 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
• 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
  • Consult the Chorus Cloud Chromatogram Extraction tip to get started.
• 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.