Table of Contents

guest
2021-09-17
Skyline Targeted Mass Spec Environment
Install 64-bit Skyline 21.1
   Install 64-bit Skyline 21.1 Unplugged
   Skyline 21.1 Administrator Install
Install 32-bit Skyline
   Install 32-bit Skyline Unplugged
Release Notes
Tutorials
   教程 (中国语文)
     靶向 方法编辑
     靶向方法优化
     分析分类研究的数据
     处理已有定量实验数据
     MS1 全扫描筛选
     并行反应监测 (PRM)
     非数据依赖型采集
     SWATH 数据分析
     小分子目标
     小分子方法开发与 CE 优化
     小分子定量
     绝对定量
     自定义实时报告
     iRT 保留时间预测
   チュートリアル(日本語版)
     ターゲットメソッドの編集
     ターゲットメソッドの最適化
     によるグループ研究データの処理
     既存データ処理および定量実験
     MS1フルスキャンフィルタ
     併発反応モニタリング(PRM)
     DIA、データ非依存性解析
     SWATHデータの分析
     によるターゲットメタボロミクス解析
     小分子メソッド開発とCE最適化
     小分子の定量化
     絶対定量
     カスタムレポートとライブレポート
     iRT保持時間予測
   Targeted Method Editing
   Targeted Method Refinement
   Processing Grouped Study Data
   Existing and Quantitative Experiments
   MS1 Full-Scan Filtering
   DDA Search for MS1 Filtering
   Parallel Reaction Monitoring (PRM)
   Basic Data Independent Acquisition
   Analysis of DIA/SWATH Data
   Small Molecule Targets
   Small Molecule Method Development and CE Optimization
   Small Molecule Multidimensional Spectral Libraries
   Small Molecule Quantification
   Hi-Res Metabolomics
   Absolute Quantification
   Custom Reports
   Advanced Peak Picking Models
   iRT Retention Time Prediction
   Collision Energy Optimization
   Ion Mobility Spectrum Filtering
   Spectral Library Explorer
   Audit Logging
   QuaSAR Quantitative Statistics
   ETH Targeted Proteomics Course Tutorials
Videos
   Video 1: Method Editing
   Video 2: Results Analysis
   Video 3: Existing & Quantitative Experiments
   Video: Trailer
Webinars
YouTube Channels
Tips
   Terminology Cheat Sheet
   Installing Skyline
     Recovering From a Broken Installation
     Recovering the .sky File Extension Association
     Running Skyline TeamCity Artifact Builds
   Small Molecules
     UI Modes
     Adduct Descriptions and Small Molecule Labels
   Getting lists of data out of Skyline
     Pivot Editor
     Document Grid Number and Date Formats
     Skyline Lists
     Result File Rules in Skyline 20.2
     Hierarchical Clustering (and PCA Plots) in Skyline-daily
   DIA (Data Independent Acquisition)
     Generating an Overlapping Window Isolation List using Skyline
     Full Spectrum Demultiplexing of Overlapped DIA Windows using MSConvert
     Import OpenSWATH Results
     Slides Explaining Data Independent Acquisition
     DIA Methods for Thermo Q Exactive
   Quantification
     Batch Calibration
     Triggered Acquisition in Skyline 20.2
     Surrogate Standards
     How Skyline Calculates Peak Areas and Heights
   Skyline System Requirements
     Parallel Import Performance
   Vendor-Specific Instrument Tuning Parameters
     Support for Bruker TOF Instruments
     SCIEX Instrument Settings
     Export SRM Methods for a Thermo LTQ
   Integration with Other Tools
     How Skyline Builds Spectral Libraries
     ID Annotations Missing with Mascot Search Results
   Share Skyline Documents in Manuscripts
     Sharing MS/MS Spectra with Manuscripts
   Miscellaneous
     Skyline Batch
     Skyline File Types and Extensions
     Waters SONAR Calibration
     Audit Logging
     Crosslinking in Skyline 21.1
     New in Skyline 4.1
     How to Display Multiple Peptides
     Ion Mobility Separation (IMS) Data
   Skyline Source Code
     How to build Skyline
Documentation
Users Meetings
Publications
   ASMS 2012 WOA am MacLean Presentation
   ASMS 2020 WOA am MacLean Presentation
Press
Awards
License Agreement
Other
   How You Can Help
   Get Involved
   3rd-Party Software
   Related
Funding
Dashboard
Team

Skyline Targeted Mass Spec Environment


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Using Skyline Batch for Large-Scale DIA

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Past

Spring May Institute - Computation and statistics for mass spectrometry and proteomics online from Northeastern U., Boston (May 3 - 14, 2021)

Spring 2021 Skyline Online (April 12- 24, 2021)

Fall 2020 Skyline Online (Oct 5 - 6 & Oct 26 - 27, 2020)

Spring Skyline User Group Meeting at ASMS online (May 27 - 28, 2020) - watch the videos!

Spring May Institute - Computation and statistics for mass spectrometry and proteomics online from Northeastern U., Boston (April 27 - May 8, 2020)

Fall Cape Town Targeted Quantitative Proteomics Course (November 18 - 22, 2019)

Fall Targeted Proteomics Course at PRBB, Barcelona (November 11 - 15, 2019)

Fall Pre-HUPO Targeted Proteomics Course in Brisbane, AU (September 9 - 13, 2019)

More Events

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User Group Meeting

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at ETH Zurich

Recently Published

Rohde, Bioinformatics - Audit Logs to enforce document integrity in Skyline & Panorama
[abstract][full-text]

Adams, Journal of Proteome Research - Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics
[abstract][full-text]

MacLean, JASMS - Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions
[abstract][full-text]

Sharma, Molecular & Cellular Proteomics - Panorama Public: A public repository for quantitative data sets processed in Skyline
[abstract][full-text]

More Publications




Install 64-bit Skyline 21.1


Thank you for your interest in using Skyline software for your targeted proteomics research or mass spectrometer quality control.




Install 64-bit Skyline 21.1 Unplugged


Welcome to the 64-bit Skyline off-line installation page, the place to download an installer which you can use to install 64-bit Skyline on computers without internet access, such as instrument control computers used for native method export and quality control data assessment. These computers must be running a 64-bit version of Windows.

Please review the license terms before installing Skyline. If you accept the terms of the agreement, click I Agree to continue. You must accept the agreement to install Skyline.



To install Skyline without internet access:

  • Download the ZIP file from this page.
  • Extract its contents.
  • Run the setup.exe file in the extracted folder.
  • If you are told you need Windows Installer 3.2, you can download it from [here].
  • If you are told you need .NET Framework 3.5 SP1, you can download it from [here].
  • If you are told you need .NET Framework 4.0, you can download it from [here].
  • If you are told you need .NET Framework 4.5.1, you can download it from [here].
  • If you are told you need .NET Framework 4.7.2, you can download it from [here].

Remember, without internet access, Skyline will not be able to tell you about new releases and automatically perform updates. You will be responsible for making any necessary updates. You are more likely to fall behind on critical bug fixes and new features. If you have internet access, it is still preferable to use the normal web installation.




Skyline 21.1 Administrator Install


The administrator install of Skyline installs in C:\Program Files.  It is used for the rare cases where an administrator needs to install Skyline on a computer that many users have accounts on, and the administrator does not want each user to have to install Skyline themselves.

Known issues:

  • Upgrading does not work. If you have an earlier version of the Skyline Administrator install, you must uninstall the previous version. If you do not do this, then the files that get installed in "C:\Program Files\Skyline" will be a nonsensical mixture of files from the two different versions, and nothing will work. You can recognize the Skyline Administrator Install in Control Panel because it looks like "Skyline (64 bit)".
  • Only an administrator can install external tools in Skyline

Please review the license terms before installing Skyline. If you accept the terms of the agreement, click I Agree to continue. You must accept the agreement to install Skyline.






Install 32-bit Skyline


The 32-bit Skyline has been discontinued since version 20.2, after its overall use had fallen below 1% of all Skyline startups.

Install 64-bit Skyline for higher memory limits. [64-bit]

You can install older versions of 32-bit Skyline unplugged for computers from our archive.




Install 32-bit Skyline Unplugged


The 32-bit Skyline has been discontinued since version 20.2, after its overall use had fallen below 1% of all Skyline startups.

Install 64-bit Skyline for the latest features and higher memory limits. [64-bit]

If you require an older version of 32-bit Skyline, please review the license terms before installing Skyline. If you accept the terms of the agreement, click I Agree to continue. You must accept the agreement to install Skyline.



To install Skyline without internet access:

  • Download the ZIP file from this page.
  • Extract its contents.
  • Run the setup.exe file in the extracted folder.
  • If you are told you need Windows Installer 3.2, you can download it from [here].
  • If you are told you need .NET Framework 3.5 SP1, you can download it from [here].
  • If you are told you need .NET Framework 4.0, you can download it from [here].
  • If you are told you need .NET Framework 4.5.1, you can download it from [here].
  • If you are told you need .NET Framework 4.7.2, you can download it from [here].

Remember, without internet access, Skyline will not be able to tell you about new releases and automatically perform updates. You will be responsible for making any necessary updates. You are more likely to fall behind on critical bug fixes and new features. If you have internet access, it is still preferable to use the normal web installation.




Release Notes


Skyline v21.1 Released on 5/27/2021

  • New! DIA-Umpire integration with library-free DIA data processing. (thanks to the Nesvizhskii lab) - [tutorial]
  • New! Skyline Batch for large-scale batch processing of data analysis with Skyline [documentation]
  • New! Class Discovery tools (hierarchical clustering and PCA plot) - [documentation]
  • Extended crosslinked peptide target support to allow any number of peptides and any number of links, especially important to monitoring disulfide bonds on antibody drug conjugates.
  • New UI for direct pasting or File > Import > Tranition List, allowing users to assign meaning to columns.
  • Improved Import > Transition List or Assay Library format detection to do a better job of detecting the list and decimal separators regardless of system number format settings.
  • Detection plot improvements.
  • New spectrum annotation button on the Full-Scan graph to allow full peptide fragment annotation on extraction spectra.
  • Added update progress display to RT > Regression and Scheduling plots.
  • Added calculated concentration y-axis on the peak area graph, found under right-click > Normalize To.
  • Added iRT support for command-line import peptide search.
  • Added View > Targets menu item to clarify how to get Targets back after closing, especially for small molecules.
  • Improved File > Share to avoid saving on unmodified documents and save directly to the .sky.zip file to avoid overwriting the file on disk for modified documents.
  • Enabled the --ui argument for SkylineCmd.exe to show the UI and allow changes that get stored in its user settings file.
  • Adding small molecules from View > Spectral Libraries where the library contains molecule list information will preserve the molecule list name.
  • Added optional display of ion mobility information in chromatogram graphs.
  • File > Export > Spectral Libraries now preserves protein and molecule list name information in the resulting .blib file.
  • Extended spectral library support:
    • Support for the latest DIA-NN speclib format.
    • Support for reading MSP-formatted spectral libraries as exported by Thermo's mzVault Viewer.
    • Support library building with .mzid.gz files and use it for MS Amanda DDA search in Skyline.
    • Support library building for invK0 attribute in pepXML written by PEAKS export.
    • Improved error message when a supported spectral library type (.msp, .sptxt, .hlf) is added as the file to use in building a library.
    • Added support for "RTINSECONDS" retention time encoding in an MSP spectral library file comment.
    • Improved error handling when trying to read a damaged BiblioSpec file.
  • Improved memory consumption during full-scan data import.
  • Added "Simple Ratios" checkbox to Peptide/Molecule Settings > Quantification settings.
  • Added new report fields:
    • Added TransitionResult.CycleTimeAcrossPeak report field.
    • Added Protein.ProteinSequenceCoverage report field with the percent of protein sequence amino acids contained in any of the peptides.
    • Added "Library Ion Mobility" report fields.
    • Added "TransitionResultIsQuantitative" and "TransitionResultIsMs1" report fields for MSstats.
  • Updated instrument vendor integration:
    • Updated Agilent method export format.
    • Updated the SCIEX WIFF2 DLLs.
    • Updated Waters MassLynx DLLs to 4.8 which returns profile IMS data with flanking zero points.
  • Ion mobility improvements found testing Thermo FAIMS support:
    • Negative CoV values now allowed.
    • On export of transition lists, CoV value now pulled from ion mobility library as needed.
    • Ion mobility libraries now support molecules described only as name+mass (was assuming a chemical formula would be available)
    • Viewing raw scan data now shows the scan's ion mobility value when available.
    • Populating an ion mobility library via "Use Results" works properly when two molecules shared the same name but different details
  • Other ion mobility UI fixes:
    • Fixed "Transition Settings > Ion Mobility > Use Spectral Library Ion Mobilities" checkbox to avoid state where it would not uncheck.
    • Full Scan graph now redraws on data reimport when showing ion mobility filter information, to ensure correct position of the purple IM filter band.
  • Fixed an issue with the Full-Scan view showing only one chromatogram type (MS1 or MS/MS) when both are available.
  • Fixed Edit Annotation form to display an error for a value list with not values specified.
  • Fixed opening or creating an ion mobility library file before the "Name" field is completed, an error pops up.
  • Fixed Import Peptide Search for PRM requiring MS1 filtering settings.
  • Fixed problem in number of methods created when exporting an isolation list or method for Thermo Fusion machines.
  • Fixed "Ratio to Heavy" to show up even if Heavy is not an internal standard type.
  • Fixed support for non-Unimod mods and terminal mods in DDA search with MS Amanda.
  • Fixed DDA search with MSAmanda to ignore FileNotFound/DirectoryNotFound when deleting temp files.
  • Fixed import peak boundaries into multi-sample wiff files.
  • Fixed pepXML spectral library building to accept search results from "peaks_db" as well as "peaksdb".
  • Fixed DDA search with MS Amanda fragment tolerance always using precursor tolerance units.
  • Fixed NullReferenceException pushing "Add" button from Result File Rules Edit List form.
  • Fixed issue with Refine >Associate Proteins with a nameless FASTA sequence.
  • Fixed unexpected error typing ')' into the empty element at the bottom of the Targets view.
  • Fixed MSFragger spectral library builder to prefer spectra from _uncalibrated.mgf to avoid de-charged fragment ion peaks.
  • Improved error message loading .skyd file when it is found to be corrupted.
  • Improved audit log hash calculation to avoid the possibility of duplication.
  • Fixed bugs with Turkish language settings mostly related to case insesitive pattern matching.
  • Fixed library build treating Mascot fixed terminal mods as not overridden by variable terminal mods.
  • Fixed an unexpected error when importing results with an ion mobility library when a precursor ion appears more than once in a document.
  • Fixed Waters "Unknown Generic Error" due to calling GetDriftTime() on functions existing in Waters .RAW but not listed in _extern.inf.
  • Fixed precursor ion spectrum support for WIFF files (use <product> element instead of <precursor>).
  • Fixed unexpected error when user specifies a DDA search in the import wizard but then uses the "Back" button to start over.
  • Improved error handling when importing small molecule transition lists with inconsistent molecule descriptions.
  • Fixed unexpected error exporting method for Bruker timsTOF.
  • Fixed bug where Protein Abundance was always #N/A if normalization method is Ratio to Heavy.
  • Fixed a bug in the small molecule UI where inappropriate text was having "Peptide" replaced with "Molecule".
  • Fixed issues in handling loss-only modifications like water and ammonia:
    • Highlighting in the Targets view for loss-only modifications.
    • Not possible to specify loss-only modifications with Edit > Modify Peptide.
    • Importing Assay Libraries with loss-only modifications on peptides requiring explicit modifcations caused an error.
  • Fixed to force choosing a filename with the same extension when a library file is missing.
  • Fixed perf and error problems with "Remove Peak" on the Document Grid.
  • Fixed irtdb docxml bug.
  • Fixed DIA isolation scheme in Import Peptide Search to use the one currently set.
  • Fixed Import Peptide Search case with no results files used to create a template document for Skyline Batch.
  • Fixed to include PeptideSettings - Filter tab settings in Library Explorer - Add All button.
  • Fixed NullReferenceException displaying tooltip on Fold Change Volcano plot if document has small molecules.
  • Fixed library build from MaxQuant search results not applying terminal label-type mods.
  • Fixed custom formats on columns in the Document Grid would be forgotten as soon as the data was refreshed.
  • Fixed Mascot variable mod override logic in library build.
  • Fixed TIC Normalization on the Peak Area Replicate Comparison graph.
  • Fixed message for opening .sky file inside a ZIP file to work when the file is in a subdirectory.
  • Fixed bug preventing DDA search with multiple files of the same name.
  • Fixed "An item with the same key has already been added" exception changing Transition Settings in a document that has a molecule with multiple precursors that are the same as each other.
  • Fixed problem where DDA search incorrectly adds isotope modifications to the document as structural modifications.
  • Fixed problem where rdotp would not appear in the Targets tree if any of the heavy transitions had zero area.
  • Fixed problem where "Accuracy" is miscalculated if the Sample Dilution Factor is not 1.
  • Fixed unexpected error if using "Modify" menu item on a molecule and changing its chemical formula to result in some precursor transitions no longer existing in the mass distribution.
  • Fixed problem where non-quantitative transitions would not show up in Peak Area - Replicates view.
  • Fixed highlighting in red "Include all matching scans" if the Acquisition Method is "Targeted" when that is the right option.
  • Improved agreement between command-line error logging and non-zero exit codes.
    • Users running Chinese and Japanese language Skyline command-line should update SkylineRunner.exe
  • Fixed Tools > Options - Miscellaneous - Clear All Saved Settings for teaching and testing.
  • Fixed a Minimize Results error if it was opened while the document was still loading.
  • Fixed a sizing layout issue in the FASTA page of the File > Import > Peptide Search wizard.
  • Fixed unexpected errors in the RT scheduling graph.
  • Fixed Library Match title to contain library name again - broken when Prosit was added.
  • Fixed --report-invariant command-line argument to always use a comma field separator.
  • Fixed Import Peptide Search to add RT predictor in if adding existing library with iRT values.
  • Fixed Import Peptide Search to always show Match Modifications page.
  • Fixed notification of iRT calculator modification when using BLIB file.

Skyline v20.2 Updated on 12/8/2020

  • Finalized Chinese and Japanese translation text
  • Fixed canceling the ion mobility library editor form when there are errors
  • Fixed some issues with background loading of ion mobility libraries (.imsdb files)
  • Fixed NullReferenceException pushing "Add" button from Result File Rules Edit List form
  • Fixed DDA search fragment tolerance always using precursor tolerance units to allow searching hybrid data
  • Fixed an unexpected error in aduct parsing

Skyline v20.2 Released on 10/13/2020

  • Integrated DDA Search (with MS Amanda) in Import Peptide Search wizard with tutorial
  • Support for crosslinked peptides (chemical crosslinking and disulfide bonds)
    • Single-line modified peptide sequence format support for crosslinked peptide targets (supported in Edit > Insert > Peptides)
      • PEPTIDEA-PEPTIDEB-[+mass@a,b]
      • e.g. PETKPESER-EKVLTSSAR-[+138.06808@4,2]
    • Support for loop-links, e.g. AKIQDKEGIPPDQQR-[+138.06808@2-6]
    • Spectral library building support for Proxl XML (http://proxl-ms.org/) of crosslink peptide seaches
  • Result File Rules - automated annotation population from result file properties including File Name and File Path
  • View > Detection > Replicate Comparison and Histogram plots for applied mProphet models
  • Qualitative ion ratio support
  • iRT improvements
    • "Automatic" option for iRT standard during library building
    • Non-linear iRT - adding Lowess and Logarithmic regressions
    • Improved iRT handling - especially with CiRT - for File > Import > Assay Library
    • Edit iRT Calculator improvements:
      • Add new IrtStandard using the current calculator's standard peptides
      • Store best transitions and relative ion abundance with calculator
  • Made Explicit Retention Time Window limit the range in which peaks are considered.
  • Support Thermo SureQuant using Transition Settings > Instrument > Triggered acquisition checkbox
  • File > Export > Method support for Bruker timsTOF prm-PASEF methods
  • IMS filtering settings moved to Transition Settings - Ion Mobility.
  • Added "Protein Results" -> "Protein Abundance" column to reports to expose the protein value used by the Group Comparison framework.
  • A new Refine > Advanced - Group Comparison tab making it easy to perform the group comparison refinement demonstrated in Webinar 8 (through Refine > Accept Peptides and a bunch of copy-paste operations)
  • Remove based on CV cutoff removes empty peptides
  • Refinement based on CV and GC can still remove proteins based on remaining peptide count
  • Added Prosit support for Propionamide (C)
  • Added a "Product Neutral Loss" column to small molecule transition list reader, which makes it convenient to describe fragments in terms of a chemical formula to be subtracted from the precursor's chemical formula.
  • Reduced the number of columns shown by default in the small molecule Insert Transition List grid
  • Import Peptide Search Wizard added from and to transition filters and min and max instrument m/z values
  • Spectral library building for the DiaNN specLib format.
  • Added support for Golm Metabolome Database GCMS spectral library in .MSP format available at http://gmd.mpimp-golm.mpg.de/
  • Support even more MSP spectral library format variants for small molecules
  • Support for specifying the analyte concentrations for each target by replicate in calibration curves with PeptideResult.ExplicitAnalyteConcentration
  • Added apply peak to group
  • Added list editing buttons to the Document Settings - Reports tab
  • Restored the ability to specify Explicit Collision Energy at the precursor level.
  • Decoys checked against targets and warning presented with ability to regenerate if they don't match closely enough.
  • Added View > Chromatograms > Close All and keyboard short cuts for Close (Ctrl-F4) and Close All (Ctrl-Shift-F4)
  • Removed limit on number of peptides and transitions during File > Import > FASTA - counting on the user to cancel the operation when it is doing more than expected.
  • Improved support for MS1-only TIC and BPC
  • New resizing progress form to show all status text
  • New report values in PrecursorResultsSummary for Detection Q Value (min, max, median)
  • Refresh of all links and images for tutorials in the Start Page - Tutorials form
  • Some performance improvements for very large DIA documents.
  • Command-line not import a raw file from the same path unless a replicate name is specified with --import-replicate-name
  • Command-line support for --decoys-discard
  • Command-line support for --refine-cv-remove-above-cutoff with decimal percent if value <1
  • Improved handling of invalid entries in spectral libraries - warn and filter instead of failing to load
  • Many smaller bug fixes such as:
    • Fixed failure to annotate fragment ions in heavy labeled Prosit predicted spectra.
    • Fixed failure to match m/z values between heavy labeled library spectra and Prosit mirror plot spectra.
    • Fixed handling of small molecule .MSP library files without Precursor_type values.
    • Fixed reading LipidBlast .MSP files from MoNA
    • Fixed support for MaxQuant's NotNTerm and NotCTerm fixed mods
    • Fixed bug where MaxQuant spectral library build failing to parse file if it is missing both optional columns "Labeling State" and "Evidence ID".
    • Fixed library build mzML -> MSFragger -> PeptideProphet pipeline (broken by previous fix to TIMS/MGF -> MSFragger -> PeptideProphet; now both pipelines work)
    • Fixed library build file extension detection to be case insensitive.
    • Fixed library build for tilde quotes ("File:~SomeRunName~") in Mascot DAT parser.
    • Fixed library build for ProxlXml parser to not require linker_mass for unlinked peptides.
    • Fixed a problem reading Agilent GCMS SIM SIC chromatograms
    • Increase the threshold scan range at which we consider an MS1 scan to be a "SIM Scan" from 200 to 500
    • Fixed SkylineCmd.exe error reporting when Skyline[-daily].exe are missing and ability to run from downloaded ZIP file without needing to unblock more than SkylineCmd.exe itself.
    • Fixed possible deadlock using SkylineCmd/Runner to import data
    • Fixed calculation of TIC when not MS1-only TIC is available - temporarily reverting to old slower Skyline code to calculate through spectrum summing - faster fix coming
    • Fixed export of negative CoV values for FAIMS methods
    • Fixed IMS display and units in reports to be consistent across PrecursorResults and Chromatogram values
    • Fixed a null reference when dealing with libraries that have inconsistent ion mobility coverage
    • Fixed errors requiring a restart switching iRT standards in the Edit iRT Calculator form
    • Fixed preserving the original standards in an iRT library when standards are changed with the dropdown list
    • Fixed warning about overwriting changes in an iRT library when none have been made
    • Fixed exception using triggered acquisition if some precursors are missing chromatograms.
    • Fixed unhandled error when importing peak boundaries for document with no result files
    • Fixed issues handling SCIEX Midas data
    • Fixed mProphet model training display to avoid empty space on the left and compressed histograms on the right.
    • Fixed "Bandwidth too small" exception doing a Loess regression if there are not enough peptides in the document.
    • Fixed LOQ determination so that it starts looking from the highest concentration point stops looking once it finds a level that fails the criteria.
    • Fixed Shimadzu method numbering
    • Fixed Ctrl-A to work as select all in the Document Grid even when it is docked.
    • Fixed loading Shimadzu SRM files with just 1 chromatogram.
    • Fixed exception bringing up RT Linear Regression window if there are crosslinked peptides in the document.
    • Implemented a workaround for 32 transition limit on Waters method functions.
    • Fixed handling a couple of novel adduct descriptions seen in the wild, e.g. "(M+H)+" and "(M+H)+[-H2O]", which would normally be written as "[M+H]+" and "[M-H2O+H]+" respectively.
    • Fixed NullReferenceException trying to use Triggered Acquisition in small molecule document.
    • Fixed retention time alignment makes mouse act out of phase on aligned replicate chromatogram graphs.
    • Fixed File > Import Assay Library recognizing sequences surrounded by underscores and preceding N-terminal modifications produced by Spectronaut.
    • Fixed pepXML reader looking for pepXML elements inside <analysis_summary>.
    • Upgraded MethodCreator.dll for Agilent method export.
      • The fragmentor voltage will be set using the voltage from the template method.
      • For proteomics applications, the recommended fragmentor voltage for G6420, G6460, G6470 instrument models is 130.
    • Fixed Panorama server checking for in-house Panorama servers.
    • Fixed tooltips on Molecule Settings form for small molecules.
    • Fixed blank IMS spectrum Full-Scan plot when shown in 2D with filtering on.

Skyline v20.1 Updated on 03/16/2020

  • Finalized Chinese and Japanese translation text
  • Fixed preserving manually set peak boundaries after reimport
  • Fixed Library Match view visibility to require a library or Prosit enabled
  • Fixed undo and audit logging of right-click > Quantitative property setting
  • Fixed command-line import deadlocking race condition
  • Fixed modification redefinition error in Import Peptide Search
  • Fixed major performance issue with lockmass correction in Waters data imports
  • Fixed command-line logic for when files get ignored during import if they have already been imported
  • Fixed Bruker data import failure issues
  • Fixed issue where Transition Settings changes could be overwritten during Import Peptide Search
  • Fixed audit logging of changes to DIA isolation schemese
  • Fixed a null reference when dealing with libraries that have inconsistent ion mobility coverage
  • Fixed exception in the iRT calibration form
  • Fixed exception doing "close all chromatograms".
  • Fixed Import Peptide Search to turn off MS1 filtering if no precursor ions
  • Fixed command-line run length to decimal value instead of an integer

Skyline v20.1 Released on 01/28/2020

  • Prosit spectrum and iRT prediction support directly integrated into the UI
    • Building libraries for targeted peptides in a document through Peptide Settings - Library - Build button.
    • Prosit spectrum prediction viewing in the Spectrum Match plot with new right-click menus, including mirror plotting
    • Settings in Tools > Options > Prosit
  • Support for spectral library building from MS Fragger pepXML search results
  • Support for diaPASEF!
    • We have run this with 2 separate 3-organism datasets through the LFQBench statistical assessment and that works.
  • Improved ddaPASEF and initial prmPASEF support.
  • Performance gains in importing Agilent and Waters IMS data as much as 2x or more.
  • Parallel file import with proteomewide DIA in the UI or by default on the command-line has performance similar to what was previously only available from the command-line using --import-process-count. Choose "Many" on your next import or just ignore threading the next time you import from the command-line.
  • Optimized spectrum memory handling for instrument vendors with .NET data reader libraries, benefitting Agilent, SCIEX, and Thermo
  • A new "Consistency" tab in the Refine > Advanced form, supporting CV and q value cut-offs
  • New checkbox for Refine > Advanced - Results tab Max precursor peak only
  • Support for Multiple Attribute Model (MAM) grouping with Peptide.AttributeGroupID and PeptideResults.AttributeAreaProportion
  • Added File.SampleID and .SerialNumber (of the instrument) as fields in Document Grid custom reports
  • Transitions Settings - Full-Scan - MS/MS filtering has been extended to apply to all non-MS1 spectra (e.g. MS3) as long as the MS1-level precursor matches the target precursor m/z The redundant library filtering phase of spectral library building is around 20x
  • Improved iRT calibration UI making it easy to create new sets of standards based on existing sets that can be used in spectral library building and the Import Peptide Search wizard
  • More iRT improvements including more intelligent use of 80+ CiRT peptides when CiRT is chosen during library building
  • New right-click > Quantitative menu item for changing the Quantitative property on transitions in the Targets view TIC and BPC now come from raw data files and do not need to be extracted from MS1 spectra which has performance benefits for MS1 filtering
  • New global "QC" transitions have been added such as the pressure trace
  • Calibration curve fixes to make ImCal (Isotopolog Calibration Curves) work
  • New "Calculated" annotations have been added which support storing Skyline calculated values in annotations for future use with AutoQC
  • Optional display of spectral library spectrum scores in Spectrum Match, View > Spectral Libraries and in Document Grid
  • Added Spectral library building support from "Assay Library" TSV
  • New View > User Interface menu item in case the user misses the toolbar button
  • New View > Peptides submenu to display modifications in the Targets view text for cases like glycan mods on biologics
  • Support for charged losses on peptide modifications like for glycan mods to monitor precursor - lost, minus charge
  • New option to order by m/z in exported methods/lists for optimized quadrupole switching Restore the ability to insert a transition list of either type when not in mixed UI mode
  • Support KEGG IDs as molecular identifiers in small molecule targets.
  • Improved support for D used in chemical formulae in place of the Skyline default H'
  • Added support for Thermo Exploris and Eclipse instruments
  • Support for opening .skyp files downloaded directly from Panorama
  • New command-line arguments:
    • --version - prints the Skyline[-daily] version information to the console
    • --save-settings - saves and settings changes made during the session (e.g. opening a document may add elements to lists)
    • --tran-predict-ce="<name>" - change the Transition Settings - Prediction - Collision energy setting
    • --tran-predict-dp="<name>" - change the Transition Settings - Prediction - Declusering potential setting
    • --tran-predict-cov="<name>" - change the Transition Settings - Prediction - Compensation voltage setting
    • --tran-predict-opt="<name>" - change the Transition Settings - Prediction - Optimization library setting
    • --import-filename-pattern - selects imported files from directory by a pattern
    • --import-samplename-pattern - selects imported samples from a multi-file WIFF by a pattern
    • --ims-library-res command-line argument for adjusting the library IMS extraction resolving power for testing varying settings on 3-organism mixes
    • --share-zip - fixed from being broken in 19.1
    • --exp-order-by-mz - orders transitions in exported methods/lists by m/z for optimized quadrupole switching
  • Strong versioning in Skyline-daily.exe and SkylineCmd.exe
    • When you hover the mouse over these EXE files in Windows File Explorer the version number is reported in a tip (no longer just 1.0.0.0)
    • The command-line --version argument now always reports a full version, even for a "developer build" including the Git hash for the source control revision on GitHub, and now the version of ProteoWizard, ensuring the pwiz_data_cli.dll can be loaded.
    • The Skyline Help > About form now also includes this full version with Git hash
  • Many smaller bug fixes such as:
    • Spectral libraries from MaxQuant results using spectra from raw data now uses the right spectra
    • Fixed BiblioSpec parser for MaxQuant 1.6.7 mod format
    • Fixed for issue with iProphet and 2H element for MaxQuant
    • Made charge state suffix parsing more flexible to handle the following cases:
      • A series of + or - symbols however long (used to stop at ++++ for positive and -- for negative)
      • Use CultureInfo.TextInfo.ListSeparator (semi-colon in Europe) "; +5" instead of CultureInfo.NumberFormat.NumberGroupSeparator (period, space or apostrophe in Europe) ". +5", " +5", or "' +5"
      • Allow invariant form always ", +5" even when current culture indicates "; +5"
      • Allow the absence of the space in charge states with numbers, i.e. ",+5" or ";+5"
    • Fixed right-click > Order By > Annotation in replicate summary plots
    • Fixed error "Spectrum must have a source file" when doing Import Assay Library tutorial
    • Fixed problem where "batch_name" was not getting written out for replicates.
    • Fixed problem where changing the uniqueness constraint in the Peptide Settings dialog does not result in a new Undo record being created.
    • Fixed error when doing "Export Annotations" if StandardType has been specified for peptides.
    • Fixed error when List has "value list" column type.
    • Exclude peptides from .elib files that do not appear in the "PeptideQuants" table.
    • Fixed missing peak logic when importing with EncyclopeDIA or OpenSWATH results
    • Added support for reading the expect score from Comet pepXML and for using ms2 files for finding spectra of pepXML files.
    • Fixed Tools > Tool Store error message when skyline.ms server is down for maintenance.
    • Fixed controls hidden on Import > Peptide Search form when initiated from the Start page.
    • Fixed problem where Skyline was not acknowledging the isolation windows on MSX scans.
    • Fixed calculation of LOD. It was incorrectly using only using the multiple of the SD of the blank values. It was forgetting to add the mean of the observed values as well.
    • Fixed Precursor Concentration getting blanked out whenever the Peptide Settings changed.
    • Fixed to support a change to the Uniprot interface for querying protein details.
    • Fixed exception when doing "Pick Children" on a small molecule that has two identical precursors.
    • Fixed "Refine > Advanced" max peptide peak rank when there are peptides that only have internal standard precursors and increase maximum peptide peak rank from 10 to 20.
    • Fixed exception that can happen if deselect EmptyNode at bottom of Targets tree while Peak Area Replicate Comparison is shown.
    • Fixed CCS calculation for Bruker data to use 2*N instead of just N.
    • Fixes to improve support for a 1.3 GB Assay Library including a fix to an OutOfMemoryException
    • Fixed progress display of upload to Panorama
    • Fixed Area CV calculation for heavy labeled ratio normalization.
    • Fixed modified peptide sequence text exported from Skyline in .blib spectral libraries to match library builds
    • Fixed unexpected error using Refine > Advanced in small molecule documents with results
    • Fixed renaming a molecule causes miscalculating mass of transition with heavy label adduct
    • Fixed File > Export > Spectral Library losing information from small molecule documents
    • Fixed case sensitivity in library file name extensions

Skyline v19.1 Released on 07/14/2019

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.

  • 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. [documentation]
    • See Document Settings – Lists
  • Batch calibration – [documentation]
  • 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

Skyline v4.2 Updated on 04/08/2019

Skyline v4.2 Updated on 01/08/2019
Skyline v4.2 Released on 11/01/2018

  • 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 plot 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 such as:
    • Fixed problem reading Thermo raw files that have scans with multiple precursors.
    • Fixed "use results" on "Edit Drift Time Predictor" form to pay attention to whether "Use high energy offset" is checked. If it's not checked, then always use 0 for the high energy offset.
    • Fixed problem where matching chromatograms to transitions does not pay attention to m/z match tolerance and double counts transitions.
    • Fixed ion mobility lookup in spectral libraries to support high precision modifications.
    • Fixed bug where documents containing the adduct "[2M+H]" cannot be opened.
    • Fixed "Remove Peak" behavior when chromatograms showing more than one file.
    • Fixed performance and background updates for Retention Times - Regression view
    • Fixed to editing small molecules with MS1 precursors that resulted in document corruption
    • Fixed to allow unchecking "Intensity" in an mProphet scoring model
    • Fixed to improve performance in a document with 500 replicates
    • Fixed to improve graphs restoring their visible state in the absence of a .view file
    • Fixed performance for large iRT libraries
    • Fixed a bug where libraries were disregarding modifications when returning retention times
    • Fixed matching spectra in SCIEX Midas data to precursors with modifications, especially heavy labeled
    • Fixed problem where a mixed polarity .raw file can result in an error about the number of times not being equal
    • Fixed obscure Thermo scanfilter parsing issue with a negative SID
    • Fixed case where ModifiedSequence would display the wrong mass if there were two modifications on the same amino acid
    • Fixed unexpected error trying to use Centroided extraction from Waters data acquired in centroid mode
    • Fixed small molecule PrecursorIonFormula vs. PrecursorNeutralFormula in small molecules with isotope labeling
    • Fixed issue with neutral loss transitions not matching spectral libraries during a settings change
    • Fixed to keep fragment ion transitions from matching chromatograms extracted from MS1
    • Fixed error message for file access denied from "Win32 Error 5" to something more helpful
    • Fixed issue with importing transition lists containing O" or 17O
    • Fixed for Waters data import to allow both centroiding and lockmass correction
    • Fixed small molecule transition list reader when Transition Settings precursor and fragment mass types are different
    • Fixed small molecule transition list import where the product columns are left empty to imp[y that the precursor is the ion of interest for this row
    • Fixed excessive memory use building a background proteome
    • Fixed issue with chromatogram extraction from mixed polarity raw data files
    • Fixed protein annotation using Uniprot to keep up with changes in their interface
    • Fixed command-line to import all samples from a multi-sample WIFF file

Skyline v4.1 Release Updated on 6/19/2018

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.




Tutorials


[Chinese] [Japanese]

Try one of these tutorials, and get hands-on experience using Skyline with real data.

Introductory

 

Full-Scan Acquisition Data



 

Small Molecules

Hi-Res Metabolomics (17 pages)


 

Advanced Topics

Custom Reports (33 pages)
Audit Logging (23 pages)

 

ETH Course Tutorials 2016 & 2018 (Skyline SRM/PRM/DIA + MSstats + mProphet tutorials with exercises)
SRM CourseETH Targeted Proteomics Course



教程 (中国语文)


[英语] [日语]

请选择尝试这些指南,以获得对实际数据运用Skyline软件的实际操作经验。

介绍性的

靶向方法编辑 (25页)

 

靶向方法优化 (26页)

 

 

 


全扫描采集数据

 


 


小分子

小分子目标 (9 页)

小分子定量 (30 页)



 


高级主题

绝对定量 (19 页)

 

更多即将推出!




靶向 方法编辑


针对靶向蛋白质组学实验亲自动手创建 Skyline 文档。在此指南中, 您将学会从 pepXML 和 mzXML 文档以及 FASTA 格式的背景蛋白质组文件中创建 MS/MS 谱图库。您将把这些信息与在 GPM 数据库网站 (Gobal Proteome Machine) 上的某个公共 MS/MS 谱图库相结合,按照指引创建全新的 Skyline 文档,对一些特定的酵母蛋白质、肽段和子离子进行靶向分析。根据此 Skyline 文档,您将导出一个离子对列表,以供直接在 AB 4000 Q Trap 型质谱仪上进行检测分析。(25 页)。

[下载]



* - Skyline 0.6 版本中开始引入, 继而分别对 1.4、2.5、3.7、20.1 版本进行了更新。

2015 年 2 月 10 日,Skyline 团队举办了第 4 场网络研讨会:Skyline 靶向方法设计,这是该基础课题的又一重要资源。

[网络研讨会]




靶向方法优化


从已发布的离子对和 SRM 质谱仪实验开始,亲自体验定量实验和同位素标记的参考肽段的处理。学习如何利用 Skyline 提供的色谱峰和色谱保留时间摘要图表,进行高效的数据分析。(26 页)

[下载]

* - Skyline 0.7 版本中开始引入,继而分别对 1.4、20.1 版本进行了更新

另外, 更多内容请参考我们发表在Proteomics 上的文章。(请引用)

The development of selected reaction monitoring methods for targeted proteomics via empirical refinement
[摘要]

2015 年 3 月 10 日,Skyline 团队举办了第 5 场网络研讨会:Skyline 靶向方法优化,这是该课题的又一重要资源。

[网络研讨会]

了解更多 关于结果检查和优化实验设计方法的内容,可以阅读我们 ASMS 2009 的海报。

ASMS 2009 Poster




分析分类研究的数据


学习如何利用skyline有效的处理在一个生理状态下多个生物样品的实验数据。你将会使用一个可以被检测到的目标列表,并进一步优化该列表,使其可以只包含在健康和生病状态下在老鼠 (14只)的血浆中具有不同浓度的分子。在这个过程中,你讲学会如何使用skyline快速的研究和理解反常数据。你也会得到一些关于如何使用Skyline (版本3.1)来比较不同生理状态的经验。本教程总共有69页。)

[下载]



* - 根据版本3.1编写的使用说明




处理已有定量实验数据


从已发布的离子对和 SRM 质谱仪实验开始,亲自体验定量实验和同位素标记的参考肽段的处理。学习如何利用 Skyline 提供的色谱峰和色谱保留时间摘要图表,进行高效的数据分析。(40 页) 

[下载]



* - Skyline 0.7 版本中开始引入,继而分别对 1.4、20.1 版本进行了更新

2015 年 12 月 1 日,Skyline 团队举办了“第 12 场网络研讨会:Skyline 中同位素标记的标准品”,这是该课题的又一重要资源。

[网络研讨会]>




MS1 全扫描筛选


动手创建 Skyline 文档,使用数据依赖采集 (DDA) 实验中的 MS1 扫描数据来测量肽段表达的定量差异。在本教程中,您将学习从探索性实验数据集中构建图谱库,为 MS1 过滤配置 Skyline 文档,导入质谱仪原始数据文件,以从 MS1 扫描中提取母离子色谱图,然后根据 MS/MS 图谱肽段鉴定信息挑选合适的色谱峰,以及利用 Skyline 进一步处理得到的定量数据。如果您对探索性实验无标记定量分析感兴趣,本教程将帮助您认识一种新的研究工具。(41 页)

[下载]

* - 1.2 版本中开始引入,然后针对 1.4 版本进行了更新,针对 2.5 版本进行了修订,继而又针对 20.1 版本进行了更新。

另外, 关于Skyline无标记定量的算法和工作流程,更多内容参考我们发表在Molecular Cellular Proteomics 上的文章(请引用该文章):
Platform independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline. Application to protein acetylation and phosphorylation
[摘要]




并行反应监测 (PRM)


使用低分辨率 Thermo LTQ 和高分辨率 Agilent 6520 Q-TOF 中获得的并行反应监测 (PRM) 数据,获取实际操作经验。利用低分辨率和高分辨率仪器中测量的母离子和碎片离子,加强对肽段定量之间的选择性和灵敏度差异的认识。运用 Skyline 提供的丰富功能探索新方法,了解自己的质谱数据,以进行基于色谱的定量蛋白质组学处理。(37 页)

[下载]



* - 1.2 版本中开始引入,然后针对 1.4 版本进行了更新,继而针对 2.5 和 20.1 版本进行了修订。

另外, 更多信息请参考我们发表在Journal of Proteome Research 上的文章(请引用该文章)
Label-Free Quantitation of Protein Modifications by Pseudo-Selected Reaction Monitoring with Internal Reference Peptides
[摘要]




非数据依赖型采集


通过一个含有非依赖型数据采集和依赖型数据采集 (在同一个仪器上采集这两种数据)的实验方法来得到分析非依赖型数据的经验。定义和导出一个非依赖型数据采集方法的隔离方案。在进行非依赖型数据采集之前,进行依赖型数据采集,并利用其结果来建立一个质谱谱图库。根据质谱谱图库来选择对应目标蛋白质的多肽和离子对。用skyline导入并分析相关的非依赖型数据采集的结果来熟悉这个实验流程。本教程总共有40页。

[下载]



* - 根据版本2.6编写的使用说明




SWATH 数据分析


Navarro, Nature Biotech 2016 基准论文为依据,使用为指示说明而创建的三物种混合数据集,获得从 Q Exactive 或 TripleTOF 仪器中采集的数据独立采集 (DIA) 数据的实际操作处理经验。对 DIA 使用“导入肽段搜索”向导以根据 DDA 数据构建谱图库,期间对保留时间校准进行自动 iRT 校准,并对肽段峰值检测采用 mProphet 学习模型。采用“保留时间”、“峰面积”、“质量精度”和 CV 等丰富的 Skyline 摘要图评估数据质量。最后进行群组比较,并对通过数据获取每个物种预期比率的效果进行评估。(31 页)

[下载 QE] [下载 TTOF]

* - 20.1 版中开始引入

2020 年 4 月 7 日,Skyline 团队举办了第 18 场网络研讨会:重新审视 Skyline 中的 DIA/SWATH 数据分析,现场演示了这种新材料。

[网络研讨会]

2017 年 1 月 25 日,Skyline 团队举办了第 14 场网络研讨会:运用 Skyline 实现大规模 DIA,重点介绍了自首次举办 DIA 网络研讨会以来 28 个月中开展的其他研究和工作流程。

[网络研讨会]

2017 年 4 月 4 日,Skyline 团队举办了第 15 场网络研讨会:使用 Skyline 优化大规模 DIA,对使用新的数据集和新的仪器类型有了新的了解。

[网络研讨会]]




小分子目标


学习如何利用 Skyline 来分析非蛋白质组小分子离子目标。您将导入用于代谢组学实验的小分子离子对列表,并从 Waters Xevo TQS 导入 14 次分析。开始学习如何将 Skyline 应用到小分子的实验中。(9 页)

[下载]

* - Skyline 3.1 版本中开始引入,然后针对 Skyline 19.1 和 Skyline 20.1 进行了更新

2015 年 2 月 10 日,Skyline 团队举办了第 14 场网络研讨会:Skyline 靶向方法编辑,率先介绍小分子支持。
[
网络研讨会]

2017 年 11 月 7 日,Skyline 团队举办了第 16 场网络研讨会:Skyline 小分子研究,讨论了用于小分子支持的新材料。
[网络研讨会]

阅读这张 MSACL 2015 海报,详细了解有关使用 Skyline 进行小分子定量的更多信息。

MSACL 2015 Poster




小分子方法开发与 CE 优化


通过文献引用了解如何创建以稳定同位素标记的小分子为目标的 Skyline 文档,这些小分子指定为母离子质荷比、子离子质荷比和碰撞能量值。通过导入来自 Waters Xevo TQ-S(使用 Sciex 三重四极杆质谱仪的初始 CE 值)的多个重复测定数据集,对小分子执行保留时间时序安排和碰撞能量优化。了解最初为靶向蛋白质组学应用而创建的 Skyline 功能中,有多少现成的功能现在可以应用于小分子数据。(39 页)

[下载]

* - Skyline 4.1 版本中开始引入,继而针对 19.1 和 20.1 版本进行了更新

2015 年 2 月 10 日,Skyline 团队举办了第 14 场网络研讨会:Skyline 靶向方法编辑,率先介绍小分子支持。
[网络研讨会]

2017 年 11 月 7 日,Skyline 团队举办了第 16 场网络研讨会:Skyline 小分子研究,讨论了用于小分子支持的新材料。
[网络研讨会]

阅读这张 MSACL 2015 海报,详细了解有关使用 Skyline 进行小分子定量的更多信息。

MSACL 2015 Poster




小分子定量


了解如何创建以小分子为目标的 Skyline 文档,这些小分子指定为母离子化学公式和加合物以及子离子质荷比值。导入在三重四极杆质谱仪上使用 LC-MS/MS 收集的多重重复测定数据集,了解最初为靶向蛋白质组学应用而创建的 Skyline 功能中,有多少现成的功能可以应用于小分子数据。 (30 页)

[下载]

* - Skyline 4.1 版本中开始引入,继而针对 19.1 和 20.1 版本进行了更新

2015 年 2 月 10 日,Skyline 团队举办了第 14 场网络研讨会:Skyline 靶向方法编辑,率先介绍小分子支持。
[网络研讨会]

2017 年 11 月 7 日,Skyline 团队举办了第 16 场网络研讨会:Skyline 小分子研究,讨论了用于小分子支持的新材料。
[网络研讨会]

阅读这张 MSACL 2015 海报,详细了解有关使用 Skyline 进行小分子定量的更多信息。

MSACL 2015 Poster




绝对定量


获取使用 Skyline 校准定量的实际操作经验,以估算实验中肽段的绝对分子量。( 19 页) 

[下载]



* - Skyline 1.1 版本中开始引入,针对 1.4 版本进行了更新,在 3.5 版本中进行了校准功能更新,继而针对 20.1 版本进行了更新

2015 年 12 月 1 日,Skyline 团队举办了“第 12 场网络研讨会:Skyline 中同位素标记的标准品”,这是该课题的又一重要资源。

[网络研讨会]

2016 年 4 月 15 日,Skyline 团队举办了“第 13 场网络研讨会:使用 Skyline 进行校准定量”,这是该课题的又一重要资源。

[网络研讨会]

另请参阅 Nature Methods 中的论文 基于经验快速发现用于靶向蛋白质组学的最佳肽段

[摘要]






自定义实时报告


借助 Skyline 自定义实时报告的能力,查看、编辑和导出 Skyline 文档中的各种值,获取实际操作处理经验。这些报告非常适合在 Excel 中使用,或在使用 R、Matlab、Java、C++ 和其他语言编写的自定义代码中使用,从而在使用 Skyline 处理仪器输出后进行深度统计分析。还可以学习在 Skyline 中检查数据时如何使用 Skyline 结果网格视图访问这些值并添加自定义注释。遵循本教程操作可极大增加使用 Skyline 完成的实验范围。 (32 页) 

[下载]



* - Skyline 0.6 版本中开始引入,然后针对 1.4 版本进行了更新,针对 2.5 版本进行了修订,继而又针对 20.2 版本进行了更新




iRT 保留时间预测


本教程将引导您获得 iRT 技术的实际操作经验。iRT 技术将校准过的、基于经验检测的肽段色谱保留时间存入一个库中,供日后针对安排时序的采集和峰检测结果的验证进行保留时间预测。在本教程中,你将学习如何校正自己的 iRT 计算器,以及详细了解关于 iRT-C18 校准的过程。其中,iRT-C18 是 BiognosysiRT-Kit 中使用的肽段标准样品。本教程将引导您利用 SRM 数据、图谱库和探索性实验 MS1 过滤得到的色谱峰校正新的 iRT 值。同时,您将学习如何重新校准这些 iRT值,对采用新梯度的新列安排 SRM 采集。本教程将展示 iRT 预测的精度,以及更高精度的保留时间预测在色谱峰鉴定结果验证中如何提供更高的可信度。((本教程共36页) 

[下载]

* - 1.2 版本中开始引入,继而分别对 1.4 和 20.1 版本进行了更新

2015 年 5 月 12 日,Skyline 团队举办了“第 7 场网络研讨会:使用 Skyline 进行 iRT 保留时间预测”,这是又一重要资源,可用于了解有关 Skyline 中 iRT 保留时间标准化和库构建概念的更多信息。
[网络研讨会]

2017 年 1 月 25 日,Skyline 团队举办了“第 15 场网络研讨会:使用 Skyline 实现大规模 DIA”,会上提出了更新的高级 DIA 工作流并使用更大规模的数据集。第 14 场网络研讨会还涉及将 iRT 集成到方法开发中。
[网络研讨会]

另外, 更多细节请参考我们发表在Proteomics上的文章 (请引用)
Using iRT, a normalized retention time for more targeted measurement of peptides
[摘要]




チュートリアル(日本語版)


[英語] [中国語]

これらのチュートリアルでは,実際のデータを用いた解析をご自身の環境で経験いただくことができます。

入門編

 

フルスキャン測定データの解析

SWATHデータの分析 (35ページ)


小分子タ

小分子ターゲット (12ページ)
小分子の定量化 (28ページ)

 

上級者向け

絶対定量 (21ページ)
iRT保持時間予測 (37ページ)

他の内容は近日公開する予定です!




ターゲットメソッドの編集


ターゲットとするプロテオミクスの実験に適したSkylineドキュメントの作成について学んでいきます。このチュートリアルでは、pepXMLとmzXMLファイルからスペクトルライブラリを作成する方法、そしてFASTAファイルからバックグラウンドプロテオームファイルを作成する方法を学びます。これらの作成したファイルにGPM (Global Proteome Machine) 公開MS/MSスペクトルライブラリを追加することによって、選択された酵母タンパク質やペプチドそしてプロダクトイオンをターゲットするようにSkylineドキュメントを更新する方法も学びます。この作成されたSkylineドキュメントからトランジションリストをエクスポートでき、AB 4000 Q Trapに使うことができます(28ページ)

[ダウンロード]



* - Skyline v0.6にて導入。 v1.4、v2.5、v3.7、v20.1で更新。

2015年2月10日にSkylineチームが作成した ウェビナー#4: Skylineターゲットメソッドデザインでは、この基本的な話題についてもう1つのリソースを紹介します。
[ウェビナー]




ターゲットメソッドの最適化


ここでは、幅広いSRMメソッドで測定されたデータを始め、装置データをインポートし、ドキュメントを最適化することについて学んでいきます。ThermoのTSQでスケジュール化せず、2000を超えるトランジションと39回のインジェクションにより測定した最適化されていないドキュメントから作業を開始していきます。まずは、39回すべてのインジェクション測定データを1つの分析としてインポートする方法を学びます。ペプチドの疎水性度による保持時間予測やMS/MSスペクトルライブラリのピーク強度の相関性を利用して測定するピークの信頼度を高めていきます。Skylineの最適化ダイアログを使用して、最も信頼性のあるピーク以外を除外していきます。このようなステップにより、1回のインジェクションで測定できるようにトランジションのリストを減らしていきます。そして、1回のインジェクションメソッドで複数の繰り返し測定の結果をインポートし確認します。(30ページ)

[ダウンロード]



* - Skyline v0.6にて導入。 v1.4、v2.5、v3.7、v20.1で更新。

私たちのProteomics誌の論文もご覧ください。(こちらを引用下さい)
The development of selected reaction monitoring methods for targeted proteomics via empirical refinement
[要約]


結果の確認やメソッドの最適化については、こちらのASMS2009のポスターもご覧ください。

ASMS 2009 Poster



によるグループ研究データの処理


大規模なデータの解析をSkylineにより効果的に処理する方法を学びます。ここでは、14匹のラットから採取した血漿での健常群と疾患群で検出したターゲットタンパク質の差がきちんと捉えられるようにしていきます。一連のデータを処理することを通じ、短時間でデータ全体を捉え、差を理解ができるSkylineの便利な画面表示を知ることができます。さらに、Skylineのバージョン3.1で導入された、Skylineによる群間の差の比較方法についても経験できます。 (73 ページ)

[download]

* - Skyline v3.1にて導入。




既存データ処理および定量実験


ここでは、公開されているSRMのトランジッションのリストと質量分析装置の測定データを用いて、Skylineにより安定同位体標識された内標準ペプチドを利用した定量分析について体験していきます。Skylineのピークエリアと保持時間のサマリーチャートを活用することで、あなた自身のデータを効果的に分析する方法を学びます。(44ページ)

[ダウンロード]



* - Skyline v0.7より導入。 v1.4、v20.1にて更新。(ドラフト版)




MS1フルスキャンフィルタ


ここでは、data dependent 測定(DDA)の実験でのMS1スキャンデータを使用して、ペプチドの発現量の差を測定するSkylineドキュメントの作成方法について体験していきます。このチュートリアルでは、まず、探索的な実験のデータ(discovery data)からスペクトルライブラリを構築します。 そして、SkylineドキュメントをMS1フィルタリング用に設定します。 次に、測定したMS1スキャンデータからプリカーサーイオンのクロマトグラムを抽出するために質量分析装置で測定した生のデータをインポートします。 クロマトグラム上の目的のピーク選択については、MS/MSによるペプチド同定情報に基づき行われ、さらにSkyline上での処理を行うことで定量テータを得ることができます。探索実験のデータを用いた標識のない定量分析に興味がある場合、このチュートリアルは研究の新しいツールとなるでしょう。41ページ)

[ダウンロード]

* - Skyline v1.2より導入。 v1.4、v2.5、v20.1にて更新。

2014年10月21日にSkylineチームが作成したウェビナー#1: SkylineによるDDAデータの活用は、SkylineでDDAデータを扱う上で役に立つリソースです。
[ウェビナー1]

2015年6月16日にSkylineチームが作成したウェビナー#8: ターゲットのDDA: Skylineの差別化統計は、DDA実験で検出された全ペプチドから開始して、検体内で変化が見えるタンパク質へと減らすターゲットを絞らない方法です。
[ウェビナー8]

2015年9月29日にSkylineチームが作成したウェビナー#10: Skylineの修飾の作業は、ペプチド修飾についての詳しい説明に加えて、PTMのインポート、同位体標識、大規模なアッセイライブラリのインポートなどの話題を扱います。
[ウェビナー10]

クロマトグラムでID注釈の表示に関する問題が生じた場合は、ヒント: Mascot検索結果でID注釈が表示されない場合を確認してください。Mascotを使用しない場合でも役立つ情報が記載されています。
[ヒント]

私たちのMolecular Cellular Proteomics誌の論文もご覧ください。(こちらを引用下さい)
Platform independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline. Application to protein acetylation and phosphorylation
[要約]




併発反応モニタリング(PRM)


ここでは、併発反応モニタリング(PRM)の方法について、低分解の質量分析装置であるThermoのLTQと高分解能の質量分析装置であるAgilent 6520 Q-TOFのデータを使って学んでいきます。分解能の異なる装置での測定によるプリカーサーおよびフラグメントイオンを利用したペプチドの定量分析における選択性と感度の違いを理解することができるでしょう。クロマトグラフィーをベースとした定量プロテオミクスを実施する中で、Skylineが提供するさまざまな機能を活用することにより、質量分析データの理解と活用のための新しい方法を発見してください。(39ページ)

[ダウンロード]

* - Skyline v1.2より導入。 v1.4、v2.5、v20.1にて更新。

私たちのJournal of Proteome Research誌の論文もご覧ください。(こちらを引用下さい)
Label-Free Quantitation of Protein Modifications by Pseudo-Selected Reaction Monitoring with Internal Reference Peptides
[要約]




DIA、データ非依存性解析


ここでは、Data-independent acquisition(DIA、データ非依存性解析)について、同一装置で取得したDIAとDDAの測定データを利用していく方法で学んでいきます。まずは、SkylineでDIAデータを処理するための「Isolationスキーム」(DIAでのプリカーサーイオンのウィンドウ幅)の設定を行い、メソッドへエキスポートします。また、実験で使用するスペクトルライブラリをDDAのデータから、DIAの測定データの取得前に作成しておきます。そして、そのスペクトルライブラリからターゲットタンパク質を分析するためのペプチドやトランジションを選択します。そして、関連するDIAのデータをSkylineにインポートし、解析することで、DIAでの作業を始めるための基本的な流れを習熟していきます。 (43 ページ)

[ダウンロード]

* - Skyline v2.6にて導入。




SWATHデータの分析


Navarro, Nature Biotech 2016のベンチマークとなる論文に基づいて、装置用に作成された有機体3種の混合データセットを使用し、Q ExactiveまたはTripleTOF装置のいずれかより取得したデータ非依存性取得(DIA)データを利用する実務経験を積みます。保持時間校正向けの自動iRT校正でDDAデータからスペクトルライブラリと、ペプチドピーク検出のmProphet学習モデルを構築するDIAには、ペプチド検索のインポートウィザードを使用します。保持時間、ピーク領域、質量精度、CVを含むSkyline概要プロットの豊富なコレクションを使用してデータ品質を評価します。最後に、グループ比較を実行し、各有機体で予想される比率をデータがうまく取得できたかを評価します。 (35ページ)

[QEをダウンロード] [TTOFをダウンロード]



* - v20.1にて導入

2020年4月7日にSkylineチームが作成した ウェビナー#18: SkylineにおけるDIA/SWATHデータ解析 を再訪は、最新資料のライブプレゼンテーションです。
[ウェビナーウェビナー]

2017年1月25日にSkylineチームが作成した ウェビナー#14: Skylineを使用した大規模DIAでは、初めてDIAウェビナーを作成してから28か月間で開発された追加の研究とワークフローについて説明しています。
[ウェビナーウェビナー]

2017年4月4日にSkylineチームが作成した ウェビナー#15: Skylineを使用した大規模DIAの最適化では、新たに追加されたデータセットと新規の装置タイプを使用した作業により得られた追加の知見について説明します。
[ウェビナーウェビナー]




によるターゲットメタボロミクス解析


ここでは、Skylineによる小分子化合物の解析について学びます。メタボロミクス研究で使用する小分子化合物のトランジションのリストとWaters社のXevo TQSで測定した14個のデータを使いながら、Skylineでどのように解析を行うかを習得していきます。(12ページ)

[ダウンロード]

* - Skyline v3.1にて導入。v19.1、v20.1で更新。

2015年2月10日にSkylineチームが作成した ウェビナー#4: Skylineターゲットメソッドの編集では、小分子サポートの先行情報をお伝えします。

[ウェビナー]]

2017年11月7日にSkylineチームが作成したウェビナー#16: Skylineの小分子研究サポートに関する新しい資料を紹介します。

[ウェビナー]

このMSACL 2015ポスターを読み、Skylineによる小分子の定量化の詳細をご確認 ください。




小分子メソッド開発とCE最適化


唯一のプリカーサーm/z、プロダクトイオンm/z、そして衝突エネルギーの値のみが指定されている文献引用から、安定同位体標識の小分子をターゲットとするSkylineドキュメントを作成する方法を学びます。また、Sciex製Triple QuadによるCE初期値を用いたWaters製Xevo TQ-Sの複数の繰り返し測定データセットをインポートすることで、小分子の保持時間スケジュール設定と衝突エネルギーの最適化を実施します。ターゲットプロテオミクス用に当初作成されたSkylineの多くの既存機能が、現在では非プロテオミクス小分子データにいかに適用されているかを学びます。(39ページ)

[ダウンロード]



* - 元はSkyline 4.1にて導入。v19.1、v20.1で更新。

2015年2月10日にSkylineチームが作成した ウェビナー#4: Skylineターゲットメソッドの編集では、小分子サポートの先行情報をお伝えします。

[ウェビナー]]

2017年11月7日にSkylineチームが作成したウェビナー#16: Skylineの小分子研究サポートに関する新しい資料を紹介します。

[ウェビナー]

このMSACL 2015ポスターを読み、Skylineによる小分子の定量化の詳細をご確認 ください。




小分子の定量化


プリカーサーイオン化学式および付加物、そしてプロダクトイオンm/z値で指定した小分子をターゲットとするSkylineドキュメントの作成方法を学びます。三連四重極でLC-MS/MSを使用して収集された複数の繰り返し測定データセットをインポートし、元はターゲットプロテオミクスに使用するために作成された既存のSkyline機能のいくつを今度は小分子データに適用できるかを理解します。 (28ページ)

[ダウンロード]



* - 元はSkyline 4.1にて導入。v19.1、v20.1で更新。

2015年2月10日にSkylineチームが作成した ウェビナー#4: Skylineターゲットメソッドの編集では、小分子サポートの先行情報をお伝えします。

[ウェビナー]

2017年11月7日にSkylineチームが作成した ウェビナー#16: Skylineの小分子研究では、小分子サポートに関する新しい資料を紹介します。

[ウェビナー]




絶対定量


実験におけるペプチドの絶対的分子量を推定するために、Skyline校正定量を使用する実務経験を積みます。 (21ページ)

[ダウンロード]



* - Skyline v1.1にて導入。v1.4にて更新。v3.5にて校正機能を更新、v20.1にて更新。

2015年12月1日にSkylineチームが作成したウェビナー#12: Skylineで同位体標識された標準では、この話題に関するもう1つのリソースを紹介します。
[ウェビナー]

2016年4月15日にSkylineチームが作成したウェビナー#13: Skylineの校正定量では、この話題に関するもう1つのリソースを紹介します。
[ウェビナー]

『Nature Methods』に掲載された論文もご覧ください。
[要約]




カスタムレポートとライブレポート


Skylineドキュメントから広範な値の表示、編集、エクスポートを行なうことのできるSkylineのカスタムライブレポートを使用し、実務作業経験を積みます。これらのレポートはExcelでの使用に最適であり、またSkylineを用いた装置出力処理後、ディープ統計分析を行なうためにカスタムコードを使用してR、Matlab、Java、C++、その他の言語で書かれています。またSkyline結果グリッドビューを使用するこれらの値へのアクセスの取得方法、Skylineでデータの検査中にカスタム注釈の追加方法について学びます。このチュートリアルに従うことで、Skylineを使用して実現可能な実験の範囲が格段に広がります。 (35ページ)

[ダウンロード]



* - Skyline v0.6より導入。v1.4、v2.5、v20.2にて更新。




iRT保持時間予測


ここでは、スケジュール化された測定やピーク同定のための保持時間予測を行うためのiRT値について学んでいきます。校正された実測のペプチドの保持時間をライブラリーに蓄積することで、将来的に活用することができます。このチュートリアルでは、iRTカリキュレータによる校正方法や、Biognosys社により提案されているiRT-C18というキャリブレーションについて、iRT-Kitのペプチド標準品を用いて詳細に学んでいきます。さらに、SRMの測定データやスペクトルライブラリ、また、探索実験におけるMS1スキャンの測定データから得られたクロマトグラムピークからもiRT値を校正していきます。さらに、新しく設定したグラジエント条件で、新しいカラムを使用してスケジュール化したSRM測定をする際の、iRT値の再校正の方法も学習していきます。また、これらを通じて、iRT値に基づいて、保持時間を正確に予測することにより、クロマトグラムのピーク同定における信頼性が向上することもわかるでしょう。(37ページ)

[ダウンロード]

* - Skyline v1.2より導入。 v1.4、v20.1にて更新。

2015年5月12日にSkylineチームが作成したウェビナー#7: SkylineのiRT保持時間予測では、SkylineにおけるiRT保持時間の正規化とライブラリー構築のコンセプトの詳細が学べるもう1つのリソースを紹介します。
[ウェビナー]

2017年1月25日にSkylineチームが作成したウェビナー#15: Skylineを使用した大規模DIAでは、最新の高度なDIAワークフローと大規模データセットの使用について説明します。ウェビナー#14でも、メソッド開発へのiRT統合について言及しています。
[ウェビナー]

私たちのProteomics誌の論文もご覧ください。(こちらを引用下さい)
Using iRT, a normalized retention time for more targeted measurement of peptides
[要約]




Targeted Method Editing


Get hands-on experience creating a Skyline document for a targeted proteomics experiment. In this tutorial, you will create a MS/MS spectral library from pepXML and mzXML and a background proteome file from a FASTA format file. You will combine these with a public MS/MS spectral library from the Global Proteome Machine to guide creation of a new Skyline document targeting selected yeast proteins, peptides and product ions. From this document, you will export a transition list, ready to run on a AB 4000 Q Trap. (26 pages)

[download]

* - written on Skyline v0.6, updated for v1.4, updated for v2.5, updated for v3.7, updated for v20.1

On February 10th, 2015, the Skyline Team produced Webinar #4: Targeted Method Design with Skyline, another great resource for this foundation topic.
[webinar]




Targeted Method Refinement


Get hands-on experience starting with a broad set of SRM measurements, importing instrument data, and refining the document. Start with an unrefined document requiring over 2000 transitions and 39 injections to measure unscheduled on a Thermo TSQ. Learn how to import all 39 injections into a single replicate. Use a hydrophobicity to retention time regression and ms/ms spectral library peak intensity correlation to improve confidence in measured peaks. Use the Skyline refinement dialog to remove all but the best transitions for the highest confidence peaks. Step through the scheduling process to reduce the document to a transition list that can be measured in a single injection. Import and view multiple replicates of the single-injection method. (28 pages)

[download]

* - written on Skyline v0.6, updated for v1.4, updated for v3.7, updated for v20.1

Also, see our paper in Proteomics (please cite)
The development of selected reaction monitoring methods for targeted proteomics via empirical refinement
[abstract]

On March 10th, 2015, the Skyline Team produced Webinar #5: Targeted Method Refinement with Skyline, another great resource for this topic.
[webinar]


Learn more about reviewing results and refining your methods by reading the ASMS 2009 poster.

ASMS 2009 Poster



Processing Grouped Study Data


Learn how to process multi-replicate study data effectively with Skyline. You will take an initial set of targets already refined as detectable and further refine this set for evidence of differential abundance between healthy and diseased subjects a study of plasma from 14 rats. In the process you will learn to use the powerful Skyline interactive displays to quickly investigate and understand data anomalies. You will also gain experience with the Skyline Group Comparison framework. (70 pages)

[download]

* - written on v3.1

On April 7th, 2015, the Skyline Team produced Webinar #6: Effective Data Processing and Interrogation with Skyline, another great resource learning this material.
[webinar]




Existing and Quantitative Experiments


Get hands-on experience working with quantitative experiments and isotope labeled reference peptides, by starting with experiments with published transition lists and SRM mass spectrometer data. Learn effective ways of analyzing your data in Skyline using several of the available peak area and retention time summary charts. (43 pages)

[download]

* - written on Skyline v0.7, updated for v1.4, updated for v20.1

On December 1, 2015, the Skyline Team produced Webinar #12: Isotope Labeled Standards in Skyline, another great resource for this topic.
[webinar]




MS1 Full-Scan Filtering


Get hands-on experience creating a Skyline document to measure quantitative differences in peptide expression using the MS1 scans from your data dependent acquisition (DDA) experiments. In this tutorial, you will generate a spectral library from a discovery data set, set up a Skyline document for MS1 filtering, import raw mass spectrometer data to extract precursor ion chromatograms from MS1 scans, with peak picking guided by MS/MS peptide identifications, and further process the resulting quantitative data in Skyline. If you are interested in label-free quantitative analysis of discovery data sets, this tutorial will give you a new tool set for your investigation. (41 pages)

[download]

* - written on v1.2, updated for v1.4, revised for v2.5, updated for v20.1

Also, see our paper in Molecular Cellular Proteomics (please cite)
Platform independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline. Application to protein acetylation and phosphorylation
[abstract]

On October 21st, 2014, the Skyline Team produced Webinar #1: Getting the Most Out of DDA Data with Skyline, another great resource for working with DDA data in Skyline.
[webinar 1]
On June 16th, 2015, the Skyline Team produced Webinar #8: DDA to Targeted: Differential Statistics with Skyline, An untargeted approach starting from all peptides detected in a DDA experiment reduced to proteins that appear to be changing in the samples.
[webinar 8]
On September 29, 2015 the Skyline Team produced Webinar #10: Working with Modifications in Skyline , with an in-depth discussion peptide modifications, importing PTMs, isotope labeling and importing large assay libraries, among other topics.
[webinar 10]

If you run into trouble seeing ID annotations in your chromatograms, be sure to consult Tip: ID Annotations Missing with Mascot Search Results. Even if you did not use Mascot, this tip may contain useful information.
[tip]




DDA Search for MS1 Filtering


Get hands-on experience starting DDA mass spectometer files, running a peptide search with MS Amanda, building a spectral library from the search results and finally extracting chromatograms for quantitative analysis from the MS1 spectra in the DDA files. In this tutorial, you will use the Skyline Peptide Search wizard to search 3 DDA data files acquired from a human whole cell lysate with the Sigma Alrich UPS1 standard mix of stable isotope labeled proteins spiked in. You will set up Skyline to extract the precursor isotope chromatograms for all detected peptides from the MS1 spectra in the data files, and you will begin to inspect the results in Skyline. (19 pages)

[download]

* - written on v20.2




Parallel Reaction Monitoring (PRM)


Get hands-on experience working with parallel reaction monitoring (PRM) data acquired on a low resolution Thermo LTQ and a high resolution Agilent 6520 Q-TOF. Gain new understanding of the selectivity and sensitivity differences between peptide quantification using precursor and fragment ions measured on low and high resolution instruments. Discover new ways to work with and understand your own mass spectrometry data using the rich feature set provided by Skyline for working with chromatography-based quantitative proteomics. (37 pages)

[download]

* - written on v1.2, updated for v1.4, revised for v2.5, revised for v20.1

Also, see our paper in Journal of Proteome Research (please cite)
Label-Free Quantitation of Protein Modifications by Pseudo-Selected Reaction Monitoring with Internal Reference Peptides
[abstract]

On January 13th, 2015, the Skyline Team produced Webinar #3: PRM Targeted Proteomics Using Full-Scan MS and Skyline, another great resource for producing and working with PRM data in Skyline.
[webinar 3]
On July 21, 2015, the Skyline Team produced Webinar #9: PRM for PTM Studies more advanced discussion that covered using PRM data from a study of modifications on histones.
[webinar 9]
On January 16, 2018, the Skyline Team produced Webinar #13: PRM Method Development and Data Analysis a more complete and modern PRM tutorial using Thermo Fusion data.
[webinar 13]




Basic Data Independent Acquisition


Get hands-on experience working with data independent acquisition (DIA) data, using a workflow that utilizes DIA and DDA runs acquired on the same instrument in series. Define and export a DIA isolation scheme. Build a spectral library from DDA data acquired before the DIA runs for the experiment. Choose peptides and transitions for a target set of proteins based on the spectral library. Import and analyze related DIA runs in Skyline to learn a simple starting workflow for beginning to work with DIA. (40 pages)

[download]

* - written on v2.6, updated for 21.1

On November 18th, 2014, the Skyline Team produced Webinar #2: Jump Start DIA Analysis with DDA Data in Skyline, another great resource for working with DIA data in Skyline.
[webinar]

On January 25, 2017 the Skyline Team produced Webinar #14: Large Scale DIA with Skyline, which highlighted the additional research and workflows developed in the 28 months since our first DIA webinar.
[webinar]

On April 4, 2017 the Skyline Team produced Webinar #15: Optimizing Large Scale DIA with Skyline, which added new insights from working with a new dataset and a new instrument type.
[webinar]




Analysis of DIA/SWATH Data


Get hands-on experience working with a data independent acquisition (DIA) data, from either a Q Exactive or a TripleTOF instrument, using a 3-organism mix data set created for instruction, based on the Navarro, Nature Biotech 2016 benchmarking paper. Use the Import Peptide Search wizard for DIA to build a spectral library from DDA data with automatic iRT calibration for retention time calibration and an mProphet learned model for peptide peak detection. Assess the data quality using a rich collectoin of Skyline summary plots including Retention Times, Peak Areas, Mass Accuracy, and CVs. Finally, performa a group comparison and make your own assessment of how well the data capture the expected ratios for each organism. (32 pages)

[download Q Exactive] [download TripleTOF]

* - written on v20.1

On April 7th, 2020, the Skyline Team produced Webinar #18: DIA/SWATH Data Analysis in Skyline Revisited, a live presentation of this new material.
[webinar]

On January 25, 2017 the Skyline Team produced Webinar #14: Large Scale DIA with Skyline, which highlighted the additional research and workflows developed in the 28 months since our first DIA webinar.
[webinar]

On April 4, 2017 the Skyline Team produced Webinar #15: Optimizing Large Scale DIA with Skyline, which added new insights from working with a new dataset and a new instrument type.
[webinar]




Small Molecule Targets


Learn how to target non-proteomic small molecule ions with Skyline. You will import a small molecule transition list used in a metabolomics experiment and import 14 runs from a Waters Xevo TQS. Start learning how to apply the power of the Skyline interface for small molecule experiments. (10 pages)

[download]

* - written on Skyline v3.1, updated for Skyline 19.1, updated for Skyline 20.1

On February 10th, 2015, the Skyline Team produced Webinar #4: Targeted Method Editing with Skyline, with a sneak peak of small molecule support.
[webinar]

On November 7th, 2017, the Skyline Team produced Webinar #16: Small Molecule Research with Skyline, with new material on small molecule support.
[webinar]

 

Learn more about using Skyline for small molecule quantification by reading this MSACL 2015 poster.

MSACL 2015 Poster




Small Molecule Method Development and CE Optimization


Learn how how to create a Skyline document that targets stable isotope labeled small molecules from a literature citation, specified as only precursor m/z, product ion m/z, and collision energy values. Perform retention time scheduling and collision energy optimization for small molecules by importing a multi-replicate data set from a Waters Xevo TQ-S using initial CE values from a Sciex triple quad. Learn how many existing Skyline features created initially for targeted proteomics use can now be applied to small molecule data. (37 pages)

[download]

* - Originally written for Skyline 4.1, updated for 19.1, updated for v20.1

On February 10th, 2015, the Skyline Team produced Webinar #4: Targeted Method Editing with Skyline, with a sneak peak of small molecule support.
[webinar]

On November 7th, 2017, the Skyline Team produced Webinar #16: Small Molecule Research with Skyline, with new material on small molecule support.
[webinar]




Small Molecule Multidimensional Spectral Libraries


Learn how analyze complex ion mobility spectrometry-mass spectrometry (IMS-MS) small molecule data using spectral libraries and ion mobility filtering. Explore a spectral library containing m/z, retention time, fragmentation, and ion mobility information, and learn how the CCS values for each molecule are used to increase the selectivity of precursor and fragment extracted ion chromatograms. (23 pages)

[download]

* - Originally written for Skyline 20.2




Small Molecule Quantification


Learn how to create a Skyline document that targets small molecules specified as precursor ion chemical formulas and adducts, and product ion m/z values. Import a multi-replicate data set collected using LC-MS/MS on a triple quadulpole, and see how many existing Skyline features created initially for targeted proteomics use can now be applied to small molecule data. (27 pages)

[download]

* - Originally written for Skyline 4.1, updated for 19.1, updated for v20.1

On February 10th, 2015, the Skyline Team produced Webinar #4: Targeted Method Editing with Skyline, with a sneak peak of small molecule support.
[webinar]

On November 7th, 2017, the Skyline Team produced Webinar #16: Small Molecule Research with Skyline, with new material on small molecule support.
[webinar]




Hi-Res Metabolomics


Learn how to create a Skyline document that targets small molecules specified as precursor ion chemical formulas and adducts. Import a multi-replicate data set collected on a Q Exactive Orbitrap mass spectrometer for a set of plasma samples, and see how many existing Skyline features created initially for targeted proteomics use can be applied to small molecule data. (17 pages)

[download]

* - originally written for Skyline v4.1, updated for 19.1, updated for v20.1




Absolute Quantification


Get hands-on experience using Skyline calibrated quantification to estimate the absolute molecular quantities of peptides in your experiments. (19 pages)

[download]

* - written on Skyline v1.1, updated for v1.4, updated for calibration features in v3.5, updated for v20.1

On December 1, 2015, the Skyline Team produced Webinar #12: Isotope Labeled Standards in Skyline, another great resource for this topic.
[webinar]

On April 15, 2016, the Skyline Team produced Webinar #13: Calibrated Quantification with Skyline, another great resource for this topic.
[webinar]

Also, see our paper in Nature Methods
Rapid empirical discovery of optimal peptides for targeted proteomics
[abstract]




Custom Reports


Get hands-on experience working with the power of Skyline custom Live Reports to view, edit and export a wide range of values from your Skyline documents. These reports are perfect for use in Excel or with custom code written in R, Matlab, Java, C++ and other languages for doing deep statistical analysis after processing your instrument output with Skyline. Also learn to use the Skyline Results Grid view to gain access to these values and to add custom annotations while inspecting your data in Skyline. Follow this tutorial to greatly increase the scope of experiments you can achieve with Skyline. (33 pages)

[download]

* - written on Skyline v0.6, updated for v1.4, updated for v2.5, updated for v20.2




Advanced Peak Picking Models


Learn more about creating and testing advanced models for matching target peptides with chromatogram peaks in Skyline. With the 2.5 release, Skyline now supports creating linear combinations of individual peak scores using the mProphet semi-supervised learning algorithm.  In this tutorial, you will learn to generate decoy peptides and transitions, create and assess mProphet scoring models, and apply them to Skyline chromatogram peak picking, both for SRM and DIA/SWATH data.  You will learn about mProphet assigned q values (adjusted p values, based on FDR) and how you can associate them with your picked peaks and export them in a custom report. (28 pages)

[download]
 

* - written on Skyline v2.5

On April 7th, 2020, the Skyline Team produced Webinar #18: DIA/SWATH Data Analysis in Skyline Revisited, a live presentation of this new material.
[webinar]

On January 25, 2017, the Skyline Team produced Webinar #14: Large Scale DIA with Skyline which included a fairly lengthy section on current peak picking strategies in DIA.
[webinar]

On April 4, 2017, the Skyline Team produced Webinar #15: Optimizing Large Scale DIA with Skyline which included more details on peak picking strategies in DIA.
[webinar]

* - written on Skyline v4.1

You can also watch the DIA/SWATH Course presentation videos which include larger scale hands-on examples.




iRT Retention Time Prediction


Get hands-on experience with iRT, a technique for storing calibrated, empirically measured peptide retention times in a library for future use in retention time prediction for scheduled acquisition and peak identity validation. In this tutorial, you will calibrate your own iRT calculator and also learn more about the iRT-C18 calibration proposed by Biognosys for the peptide standards in their iRT-Kit. You will calibrate new iRT values from SRM data, a spectral library and chromatogram peaks filtered from MS1 scans in a discovery experiment. And, you will learn how to recalibrate these iRT values to schedule SRM acquisition on a new column with a new gradient. You will see how more accurate retention time prediction based on iRT can give you higher confidence in your chromatogram peak identity validation. (36 pages)

[download]

* - written on v1.2, updated for v1.4, updated for v20.1

On May 12, 2015, the Skyline Team produced Webinar #7: iRT Retention Time Prediction with Skyline, another great resource to learn more about iRT retention time normalization and library building concepts in Skyline.
[webinar]

On January 25, 2017, the Skyline Team produced Webinar #15: Large Scale DIA with Skyline with updated, advanced DIA workflows and using larger data sets. Webinar #14 also touches on iRT integration into method development.
[webinar]

Also, see our paper in Proteomics (please cite)
Using iRT, a normalized retention time for more targeted measurement of peptides
[abstract]




Collision Energy Optimization


Get hands-on experience using Skyline to work with empirically measured optimal collision energy (CE) values. In this tutorial, you will create scheduled CE optimization transitions lists for a document with 30 peptide precursors. Using supplied RAW files from a Thermo TSQ Vantage, you will recalculate the linear equation used to calculate CE for that instrument. You will also export a transition list with CE values optimized separately for each transition. (12 pages)

[download]

* - written on Skyline v0.6, updated for v1.4, updated for v20.2

Also, see our paper in Analytical Chemistry (please cite)
Effect of Collision Energy Optimization on the Measurement of Peptides by Selected Reaction Monitoring (SRM) Mass Spectrometry
[abstract]




Ion Mobility Spectrum Filtering


Get hands-on experience using Skyline to work IMS-TOF data. Build an ion mobility library for BSA spiked into yeast, and see how ion mobility separation improves the selectivity of chromagram extraction in complex data. Learn how to work with ion mobility data in Skyline and explore the 3D (m/z, IMS, intensity) spectra produced by IMS-enabled mass spectrometers. (26 pages)

[download]

* - written on Skyline v3.7, updated for v20.2

On April 23rd, 2020, the Skyline Team produced Webinar #19: Ion Mobility Spectrum Filtering in Skyline, another great resource for this advanced topic.
[webinar]

Also, see our paper in Journal of The American Society for Mass Spectrometry (please cite)
Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions
[abstract]

Also, see Brendan's presentation at the 2015 Agilent User Meeting at ASMS
Also, see Erin's presentation slides from the 2015 Skyline User Meeting at ASMS
Also, see the full data set on Panorama Public




Spectral Library Explorer


Get hands-on experience working with the Skyline Spectral Library Explorer. Learn more about working with isotope labels and product ion neutral losses using MS/MS spectral libraries containing 15N labeled and phosphorylated peptides. Use the Library Explorer to accelerate the transition between shotgun discovery experiments and targeted investigation. (22 pages)

[download]

* - written on Skyline v0.7, updated for v1.4, updated for v20.2




Audit Logging


Get hands-on experience working with audit logging in Skyline. Learn how to produce fully audit logged Skyline documents to help others reproduce your research, and you to remember what you did, helpting with the writing of your methods sections for publication. Learn how to work with the Audit Log grid view, an extension of the Document Grid to explore logged changes and provide reasons for the changes you make. This example uses a calibration experiment to show logging of settings changes, data import, integration adjustments, and exclusion of points from a calibration curve. Finally, you will upload your document to Panorama and see how the audit log is captured for review through a browsable web interface. (23 pages)

[download]

* - written on Skyline-daily v20.1.1




QuaSAR Quantitative Statistics


Preferred use of QuaSAR has changed from a GenePattern web page to a Skyline External Tool, installable and directly integrated into Skyline.

[download]




ETH Targeted Proteomics Course Tutorials


In 2016, members of the Aebersold lab at ETH, Zurich - with help from CRG, University of Washington, Purdue and Biognosys - presented the last week long course on targeted proteomics with SRM, PRM and DIA to 30 participants. During the course, the participants worked through 9 tutorials with follow-up exercises. This material has been made freely available on the Targeted Proteomics Course web site, providing a great resource to anyone interested in learning more about Skyline method editing and data processing (8 Skyline + MSstats + mProphet tutorials)

[go there] (2016)

Targeted Proteomics CourseETH Targeted Proteomics Course

* - written on Skyline v3.5

You can also watch the presentation videos.


In 2018, many of the same instructors with some new additions presented the second week long course on DIA/SWATH for proteomics to 50 participants. That course included new tutorials and lectures aimed at teaching DIA/SWATH data processing and use in proteomics research, with some very nice examples using Skyline. You can download them form the same location.

[go there] (2018)

DIA/SWATH CourseETH DIA/SWATH Course

* - written on Skyline v4.1

You can also watch the DIA/SWATH Course presentation videos.




Videos


Watch one of these instructional videos for a quick start using Skyline in your targeted proteomics experiments.  Although these three videos were recorded in 2009 and refer exclusively to the Skyline SRM support, they still provide a good bit of useful information about Skyline and how it may be used in setting up targeted proteomics experiments, even when using full-scan mass spectrometers.  For a more complete overview what you can do with Skyline, please refer to the Skyline tutorials.

Learn more about creating SRM/MRM methods in 28 minutes.

Video DemoVideo Demo 1

Learn more about results analysis and method refinement in 25 minutes.

Video DemoVideo Demo 2

Learn more about importing existing experiments and isotope labeled reference peptides in 27 minutes.

Video DemoVideo Demo 3

Watch the Skyline trailer video

Video TrailerVideo Trailer



Video 1: Method Editing


Try the Targeted Method Editing tutorial, and get hands-on experience.

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Download the full video for faster access to repeat viewing.

* - recorded using Skyline v0.2




Video 2: Results Analysis


Try the Targeted Method Refinement tutorial, and get hands-on experience.

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Download the full video for faster access to repeat viewing.

* - recorded using Skyline v0.5 Preview




Video 3: Existing & Quantitative Experiments


Try the Existing and Quantitative Experiments tutorial, and get hands-on experience.

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Download the full video for faster access to repeat viewing.

* - recorded using Skyline v0.5 Preview




Video: Trailer


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Created by Alex MacLean



Webinars


The Skyline Team is excited to continue its tutorial webinar series designed to help you get the most out of Skyline targeted proteomics software. Now with nineteen sessions completed, Skyline Team members spend most of the time in these webinars explaining what the software is capable of and how best to use it to answer your research questions.

Each webinar has its own page (linked below) containing a recording of the webinar and all related information. The webinar recordings are about 90 minutes long with the last 30 minutes dedicated to Questions and Answers from the attending audience. Additionally, each webinar page contains the presentations, supporting tutorial data, written answers to the Q&A sessions and other related information. Even the most experienced Skyline users are likely to learn something new.

2021

 

2018 & 2020

 

2017 & 2016

 

2015

 

2014

 




YouTube Channels


Visit Skyline's own YouTube Channel for content from recent UW courses as well as Skyline-related instructional content from courses offerered at other institutes:




Tips





Terminology Cheat Sheet


At the recent Targeted Proteomics Course at UW 2014, participants claimed that the many terms we have in mass spec proteomics with exactly the same meaning made the course much more difficult to follow.  They requested a glossary or cheat sheet that might help them translate between these various terms.  Here it is:

SRM - Selected Reaction Monitoring (sometime confused as Single Reaction Monitoring - no such thing).  Common synonym MRM (Multiple Reaction Monitoring).  Performed on triple-quadrupole instruments, where the instrument cycles through a pre-specified set of precursor m/z (Q1), product m/z (Q3) pairs called 'transitions', using the quadrupoles as filters (usually 0.5 to 1.0 m/z range).  Cycle time is determined by the sum of the dwell times of all transitions in the set.
MRM - Multiple Reaction Monitoring, a synonym for SRM created and trademarked by AB SCIEX, but extremely popular because of early popularity of AB Q TRAP instruments for performing this method.
scheduled-SRM = scheduled-MRM = dMRM = dynamic-MRM - In order to allow measuring a greater number of transitions in a run, transitions are specified with start and end times (or retention times and windows) to allow the instrument to measure each transition for only a fraction of the entire gradient.  Cycle time at any given time is determined by the sum of the dwell times of all transitions being measured at that time.
iSRM = intelligent-SRM = triggered-SRM = triggered-MRM = tMRM - In order to gain more confidence in the correct identification of a chromatogram peak in SRM without overly sacrificing quantitative throughput, the instrument measures a set of primary transitions, as in normal SRM/MRM until the intensity on those transitions exceeds some threshold.  When the threshold is exceeded, the instrument takes one or more measurements of a secondary set of transitions usually used only for peak identity confirmation, and not quantification. 

Targeted MS/MS = tMSMS = PRM = MRM-HR - Like SRM, but performed on a full-scan instrument (ion-trap or Q-TOF).  The instrument cycles through a pre-specified set of precursor m/z values, using quadrupole or ion trap isolation as a filter (usually 1.0 to 2.0 m/z range) and collects a full MS/MS fragment ion spectrum for each.  Cycle time is determined by the sum of the dwell/accumulation or scan times of all scans in the set.  Software is used to extract chromatograms from the resulting MS/MS spectra.  If the spectra are high-resolution, then extraction can be done using 50-100pm range, making it more selective than SRM.  Common synonyms PRM (Parallel Reaction Monitoring), MRM-HR (HR = High Resolution), pSRM (Pseudo Selected Reaction Monitoring).

MS1 [Full-Scan] Filtering - Chromatograms are extracted from the MS1 scans of normal DDA (Data Dependent Acquisition) data.  Because of the semi-random sampling approach, for MS/MS, of DDA, it is not possible to extract product ion chromatrams (time, intensity) with meaningful peaks for quantification.  Chromatogram-based quantification from DDA runs is limited to extracted ion chromatograms from the MS1 survey scans of such runs.  Common synonym Label Free Quant.

DIA = SWATH = HRM - Data Independent Acquisition is a technique where ranges of precursor m/z are isolated and subjected to fragmentation in a consistent pattern over cycles of time.  In this way a mass spectrometer can be set up to gather fragment ion spectra for large regions of precursor m/z space, independent of the actual precursor ions being fragmented, which may include fragments for multiple precrusors in any given scan.  Software can be used to extract product ion chromatograms from the acquired MS/MS spectra.  Cycle time is determined by the sum of the dwell/accumulation or scan times of all scans in the set.  (e.g. 20 ranges x 10 m/z = 200 m/z total range, 30 ranges x 20 m/z = 600 m/z total range)
SWATH - Popular synonym for DIA coined in Gillet, et al. MCP 2012, but also trademarked by AB SCIEX, originally specified as 32 x 25 m/z ranges covering 400 - 1200 m/z.
HRM - Hyper Reaction Monitoring, less common synonym for DIA/SWATH.
MSe - Type of DIA where ions are collected without prior filtering in alternating low- and high-energy scans (all precursors and fragments of all precursors respectively), coined and trademarked by Waters.  Common synonym All-Ions DIA.




Installing Skyline





Recovering From a Broken Installation


If you know your current release is out of date, but Skyline has not asked to upgrade after two restarts, you should first try simply manually installing again from the web page over the top of your existing installation. If this does not work, read on.

At times a Skyline installation may become so broken that you cannot install a new release over the top of your existing installation.  In this case, you will need to find the Skyline installation files on your computer, save your Skyline settings, and then either uninstall or potentially even delete the Skyline files before you can re-install and subsequently restore your settings.  This tip will walk you through doing just that.

Finding and Saving Your Settings

First, you need to find your Skyline installation.  On Windows 7 or Windows Vista, you first want to find the folder:

C:\Users\brendan\AppData\Local\Apps\2.0

On Windows XP, it will be something like:

C:\Documents and Settings\brendan\Local Settings\Apps\2.0

If you are unable to find either the AppData (Windows 7 and Vista) or the Local Settings (Windows XP) folder, you may need to do the following in Windows Explorer:

  • Press Alt+T, O to open the Folder Options form.
  • Click the View tab.
  • Under the Hidden files and folders item, click the Show hidden files and folders option.
  • Click the OK button.

You should now be able to see the necessary folder in Windows Explorer.

To save your Skyline settings before removing the Skyline files, do the following:

  • Use Windows Explorer to search within the Apps\2.0 folder for the file 'user.config'. (Starting at C:\ will be a very long search!)
  • If you find more than one, look at the Date Modified and In Folder fields to determine which is the most recent under a folder beginning with 'skyl..'.
  • Hold down the Ctrl key on your keyboard, click the mouse cursor on the file and drag it to your desktop.

Now you have a copy of your Skyline settings on your computer desktop.

Removing Skyline From Your System

The next thing you should try is to simply uninstall Skyline, using the Control Panel ("Uninstall a program" in Windows 7 & Vista, and "Add/Remove Programs" in Windows XP).  If the uninstall fails, then you have no option but to clean up manually.

Before attempting to delete your Skyline installation, you should expand the folders below the '2.0' folder, so that you seem something like the folder tree shown in the image below:

Skyline installation folders

If your '2.0' folder looks much the same as the one above, then you can simply delete the entire '2.0' folder now, but be very careful with this option, as you may have other software in here.  If you see any differences, delete only the folders beginning in 'skyl..'.

Re-installing Skyline and Restoring Settings

You have removed Skyline from your system.  After restarting the system, try again to install Skyline from the Skyline web site or stand-alone installers.

After you have installed successfully, close the Skyline window.  Then again find the 'user.config' under '2.0', belonging to a folder beginning with 'skyl..' and copy the user.config you saved to your desktop over the top of the new user.config, which will contain only the default settings.

You should now be able to start Skyline and see that your settings have been preserved, and continue working with Skyline as normal.




Recovering the .sky File Extension Association


If you end up in a state where you can no longer double-click in the Windows Explorer on .sky or .skyd files and have Skyline open the files for you, do the following:

  • Run regedit.exe and delete the following keys if any are present (they may not all be)
  • Delete the keys HKEY_CLASSES_ROOT\.sky and HKEY_CLASSES_ROOT\.skyd
  • Delete the keys HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\FileExts\.sky and .skyd
  • Delete the keys HKEY_CLASSES_ROOT\Skyline.Data.0 and HKEY_CLASSES_ROOT\Skyline.Document.0
  • Reboot your computer
  • Wait for an update or reinstall Skyline (see also Recovering From a Broken Installation)

Thanks to Stack Overflow for this entry:

https://stackoverflow.com/questions/6489112/clickonce-deployment-file-association-not-registering




Running Skyline TeamCity Artifact Builds


To download a TeamCity artifact for a feature or bugfix that will be integrated into Skyline (if a developer has provided you with a link, simply download SkylineTester.zip and skip to the next section):

  • Find the relevant pull request on GitHub: https://github.com/ProteoWizard/pwiz/pulls
  • If the TeamCity builds have not been run, wait for them to run.
  • Click the "Details" link for the "Skyline master and PRs (Windows x86_64)" build.
  • Click the "Artifacts" tab.
  • Click "SkylineTester.zip" to download.

Running the build:

  • Extract the contents of the SkylineTester.zip.
  • Run the extracted executable "SkylineTester Files\Skyline-daily.exe". No installation is necessary, because Skyline is a side-by-side exectuable and will find necessary files relative to the location of the executable.



Small Molecules





UI Modes


Skyline was built from the ground up as a proteomics targeted mass spec research tool. By popular demand, Skyline’s support for more general biomolecular mass spectrometry research has steadily increased over the past several years.

Unfortunately until the Skyline 19.1 release the user interface remained proteomics-centric. Non-proteomics researchers had to think “molecule” while seeing “peptide”, and it wasn’t always easy knowing which parts of the UI didn’t apply to your work. This was especially true for new users.

But now, Skyline adjusts its user interface according to the kind of molecules you're working with.

For full details continue reading the attached PDF.




Adduct Descriptions and Small Molecule Labels


(This tip applies to Skyline-Daily 3.7.1.11357 and later)

Ionization in Peptides vs Ionization in Small Molecules

Skyline assumes protonation for peptides so we can simply speak about "charge" or "charge states". For generalized molecules, we have to think about all kinds of ionization so we speak in terms of "adducts". Adduct descriptions may also specify isotope labels applied to the neutral molecule description. As such, "adducts" are similar to the idea of "modifications" in the peptide regime. 

Describing Ionizing Adducts

Skyline uses the defacto standard notation for ionizing adduct descriptions, as found at the Fiehn Lab's MS Adduct Caclulator and the GNPS Spectral Library. This notation has a few major parts:

Usually beginning with a left brace "[",

then an optional  dimer/trimer/etc specification,

then an "M"

then an optional isotope label specification,

then the chemical formula of the adduct,

then a closing right brace "]".

Describing Labeled Versions of Molecules for Quantification

For quantification of heavy/light pairs, Skyline expects to see a single molecule with heavy and light adduct descriptions. For example you might describe the light ion as having adduct [M+2H] and its heavy counterpart as having adduct [M4D+2H] (double protonated, and four H replaced by D). Here is a transition list describing that scenario:

Molecule,Precursor Formula,Precursor Adduct
Caffeine,C8H10N4O2,[M+H]
Caffeine,C8H10N4O2,[M4D+H]

The important point is that it describes a common molecule with distinct adduct descriptions, one of which includes labeling information.

Simple Examples

Singly protonated: [M+H]

Doubly deprotonated: [M-2H]

Sodiated: [M+Na]

N-Mer Examples:

Sodiated dimer: [2M+Na]

Deprotonated trimer: [3M-H]

Isotopic Label Examples

Sodiated, and two carbons per molecule replaced with C13: [M2C13+Na]

Sodiated, and two carbons per molecule replaced with C13, and three nitrogens replaced with N15: [M2C133N15+Na]

Charge-Only Examples:

Often transition lists are presented as m/z values with integer charges only, and the actual mode of ionization can not be inferred. In these cases we just give an integer charge value.

Unknown ionization mode, charge = 1: [M+] or [M+1]

Unknown ionization mode, charge = -2: [M-2]

Charge-Only Examples with Isotope Labels Described Only by Mass:

Sometimes a transition list indicated different precursor m/z values for the same named molecule, Skyline reads this as an isotope label of unknown formula, and expresses the mass shift as a number.

Unknown ionization mode, charge = 1, and mass shift due to unknown isotopes of total mass 5: [M5.0+]

 

 

 




Getting lists of data out of Skyline


The Document Grid and Custom Reports are the way to get lists of data out of Skyline.




Pivot Editor


The pivot editor lets you combine rows in the Document Grid, and perform aggregate operations on them such as "Mean" or "StdDev".

 

Here are some examples of how to use the Pivot Editor.




Document Grid Number and Date Formats


The Document Grid allows you to specify formats for columns that contain numbers or dates, or other formattable data types.

To set the format of a column, right-click on it and choose "Number Format...".

The "Choose Format" dialog allows you to specify a custom format string.

Microsoft provides documentation for custom number format strings and date format strings.

If you want to save your formatting choices with your custom report, you can use the "Remember Current Layout..." menu item, which is on the Group/Total button next to the Reports dropdown on the toolbar at the top of the Document Grid.

 

When a report is exported for external tools, the format used for all numeric columns is always the round-trip format ("R"), which provides the full precision possible for the numeric values. This is the format that is used if you choose "Invariant" as the language when exporting a report at "File > Export > Report".




Skyline Lists


Skyline 19.1 added new feature "Lists" which allows you to add arbitrary lists of data to a Skyline document.




Result File Rules in Skyline 20.2


Skyline 20.2 will have a new feature called "Result File Rules" which allow you to automatically set annotations and other properties by matching parts of the result file names.

[pdf]




Hierarchical Clustering (and PCA Plots) in Skyline-daily


Skyline version 21.1 will include hierarchical clustering features.

 

These features can be accessed from the Document Grid, as well as Group Comparison grids.




DIA (Data Independent Acquisition)





Generating an Overlapping Window Isolation List using Skyline


(This tip relates to Skyline v 4.2 or later.)

This is a quick demonstration on how to use Skyline to generate an overlapping-window isolation window list suitable for acquisition using the approach described in this manuscript and downstream computational demultiplexing.

To begin this demo, start with a blank Skyline document: 

  • From the Skyline landing page, click Blank Document

  • On the Settings menu, click Transition Settings and in the Transition Settings dialog box, click the Full Scan tab.

SkylineFullScan 

  • Under MS/MS filtering, click the Acquisition method dropdown and select DIA. 
  • For the Isolation scheme, select Add ...

 SkylineAddIsolation

  • In the Edit Isolation Scheme dialog, enter a name for the Isolation scheme such as '20mz_overlap' and then click the Prespecified isolation windows radio button.  

SkylineIsolationScheme 

  • Click the Calculate ... option and enter parameters for the method.  
  • Enter '500' for Start m/z.
  • End m/z is '500'.
  • Window width should be '20'.
  • Be sure that Deconvolution is set to Operlap and that Optimize Window Placement is checked.

SkylineCalculationIsolation

  • Click OK to close the Calculate Isolation Scheme dialog and OK to close the Edit Islation Scheme window.
  • Click OK once again to close the Transition Settings dialog.
  • From the main Skyline menu, select File and then Export.  From the flyout menu, click the Isolation List ... option. 

SkylineExport1

  • In the Export Isolation List window, select the appropriate instrument (for this example, 'Thermo Q Exactive') and choose a file location in which to save the list of isolation windows.

SkylineExport2 

The resulting isolation list contains the isolation centers of each isolation window in the order that they should be acquired. NOTE: the isolation centers will need to be regenerated using this approach if any of the other acquisition parameters such as isolation width or m/z range covered are changed.





Full Spectrum Demultiplexing of Overlapped DIA Windows using MSConvert


(This tip relates to Skyline 4.2 and later.)

This is a quick demonstration on how to use MSConvert to generate a demultiplexed dataset from an input datafile(s) containing spectra with overlapping data independent acquisition windows. In the case of the overlapped window approach described in this manuscript, the output from MSConvert will contain twice as many spectra as the input (two demultiplexed spectra are generated from each acquired MS/MS spectrum). This tutorial uses MSConvert distributed with ProteoWizard version 3.0.18328 with vendor libraries downloadable here: http://proteowizard.sourceforge.net/download.html

 

  • Open MSConvert and select the Browse option to select the input overlap-multiplexed files.  
  • Select the SIM as spectra option.

msconvert1

 

  • OPTIONAL: Change the output format for the file using the Output format drop-down menu. This tutorial outputs mzML.
  • Add a Peak Picking filter to the data by selecting the options indicated below and clicking the Add button below the Filters section:

msconvert2

This causes the MS2 data to be centroided prior to demultiplexing, which is currently a requirement for full-spectrum demultiplexing using MSConvert. If the data were acquired with centroiding enabled, this step will have no effect and demultiplexing will proceed as expected.

 

  • In the Filters section, add a Demultiplex filter with optimization set to Overlap Only  with the settings shown below. 
  • Click the Add button.

msconvert3

 

Note that the mass error may need to be adjusted depending on instrument platform. The mass error should be set to the maximum error expected in m/z measurement of the same analyte in subsequent spectra. Note that this measurement is of expected deviation of a measurement from spectrum to spectrum, not its deviation from the correct theoretical m/z (mass accuracy).

  • Click Start to output demultiplexed files.





Import OpenSWATH Results


NEW! in Skyline 4.2: You can now import OpenSWATH results either from TSV or OSW file into Skyline for data visualization and beginning the targeted method refinement process.

See the PowerPoint slides attached below and watch the video from the ETH DIA/SWATH course:




Slides Explaining Data Independent Acquisition


Powerpoint slides with useful information on the fundamentals of Data Independent Acquisition (DIA) are provided below.

Introduction to Data Independent Acquisition

DIA Method Design

DIA Data Analysis

Future Directions of DIA

Please note that these slide decks are incomplete because slides containing unpublished data have been removed.  If you would like the full slide deck for your personal use, or would like to use some of these slides in your own presentation, please contact the MacCoss Lab at: info@maccosslab.org

Additional material on DIA:

DIA Tutorial

DIA Methods for Thermo Q Exactive

DIA Webinar




DIA Methods for Thermo Q Exactive


The attached mini-tutorials explain how to set up DIA methods for the Thermo Q Exactive instrument:




Quantification


Calibrated quantification (a.k.a. absolute quantification) has been added to Skyline in version 3.5. We plan on extending documentation of this feature in the future in a number of ways:

  1. Updating the existing Absolute Quantification tutorial
  2. Writing a new tutorial on calibrated quantification that covers all of the available applications
  3. Including a detailed demonstration of the functionality in a future webinar

Until this work can be completed, however, you can find attached to this page a set of PowerPoint slides which hopefully provide enough of a rough overview of what is now possible that anyone interested can at least get started with the new functionality.

Also, the Skyline Tutorial Webinar #12 gives some initial coverage on this feature near the end of the recording (and in presentation slides).




Batch Calibration


Skyline 19.1 allows you to specify the "Batch Name" on replicates so that different replicates will use a different set of external standards.

See the attached PowerPoint to see how to use this feature.




Triggered Acquisition in Skyline 20.2


As of Skyline-Daily 20.1.1.83, Skyline-Daily has support for "Triggered Acquisition" methods.

A Triggered Acquisition method is one where the mass spectrometer has been told to begin collecting MS2 scans for one analyte when the mass spectrometer sees particular transitions for a different precursor.

This will enable Skyline to work better with assays such as Thermo's SureQuant Targeted Mass Spec Assay Kits

The Transition Settings > Instrument tab will have a "Triggered Acquisition" checkbox which tells Skyline that there may be large gaps between the points in an analyte's chromatograms.

When Triggered Acquisition is selected, Skyline will detect these gaps and make sure that integration boundaries do not cross these gaps. Also, Skyline will perform no background subtraction when Triggered Acquisition is enabled.

For more information, see the attached PowerPoint.




Surrogate Standards


Sometimes you want to normalize a particular analyte against a different molecule. Skyline supports this with the "Surrogate Standard" feature.

To designate that a molecule can be used as a surrogate standard, right click on the molecule in the Targets tree and choose "Set Standard Type > Surrogate Standard".

You have to use the Document Grid to change the normalization method of the analyte. The "Normalization Method" column is not shown by default, so you need to customize a view in the Document Grid and add that column. You can start by choosing "Peptides" from the Reports dropdown on the Document Grid. Then, choose "Customize Report" and add the "Normalization Method" to the view. The Normalization Method column is under "Proteins > Peptides". (also note the button at the top with the binoculars icon can be used to find columns by name)

If you have surrogate standards in your document, then the "Normalization Method" column will have options of the form "Ratio to surrogate..."




How Skyline Calculates Peak Areas and Heights


Definition:

  1. Background height: minimum intensity at peak boundaries
  2. Background area (named Background):
    • rectangular area of background height times the length between peak boundaries (pre-v1.4 patch 1)
    • total integrated area of the minimum of background height and intensity at each point (v1.4 patch 1 and later)
      (Note: the unit of RT time is second for this calculation)
  3. Peak height (named Height): maximum intensity between peak boundaries minus background height
  4. Peak area (named Area): total integrated area within peak boundaries minus background area (Note: the unit of RT time is second for this calculation)
    • area can be zero and background greater than total raw area (pre-v1.4 patch 1)
    • area plus background always equals raw area (v1.4 patch 1 and later)

NOTE: Skyline uses points that have been linear interpolated from the raw data onto a uniform interval over the duration of the chromatogram in detecting its peak boundaries and calculating its peak areas. These are also the points Skyline displays in its chromatogram graphs. Skyline uses several types of smoothing (1st derivative, 2nd derivative and Savitzky-Golay) in order to place its automatically calculated peak boundaries. These smoothed curves are available for display in the Skyline chromatogram graphs. Skyline does not, however, use smoothed data in calculating peak areas (or area under the curve - AUC). It always uses the raw interpolated points presented in the unsmoothed graphs.

Example of calculation of peak height and background area:

 

Note: with v1.4 patch 1 and higher the light blue areas are not included in the background area.





Skyline System Requirements


OPERATING SYSTEM:

Skyline runs on Windows 7 or later. 

Skyline is tested nightly on 64-bit Windows 7 and 64-bit Windows 10. Most of our development is on Windows 10 (and 7), but we know of no reason Windows 8 and 8.1 shouldn't work. 

We test the 32-bit Skyline build, but not regularly on a 32-bit OS, and < 10% of Skyline use is now 32-bit. We are likely to phase out 32-bit builds sometime in 2019.

Skyline 2.6 was the last version to support Windows XP. (All versions of Skyline since 1.4 can be downloaded from "Unplugged" installation pages by clicking "I Agree" and then the "Archive" link.)

 

PROCESSOR, MEMORY AND DISK:

There is no minimum requirement, but for performance reasons a large fast hard drive is desirable.  The amount of memory needed depends on the size of your experiments, but 4GB is a good start. Skyline is frequently taught on relatively average modern laptops. But, for larger-scale processing we recommend a more powerful desktop system with dual 24-inch monitors to take full advantage of Skyline display capabilities.

We recommend modern i7 quad-core processors, running at 3.5 to 4.0 Ghz work well, with 16 to 64 GB of RAM and a fast SSD (e.g. 500 GB) + a spinning HD with more room (e.g. 2 TB).

A modern option as of June 2021 of the type favored by Skyline developers can be found on Amazon:

Dell XPS 8940 Tower Desktop Computer - 10th Gen Intel Core i7-10700 8-Core up to 4.80 GHz CPU, 64GB DDR4 RAM, 2TB SSD + 4TB Hard Drive

For really large-scale projects, like hundreds of DIA or DDA files with many hundreds of thousands of transitions, Skyline now makes effective use of highly multi-processor (NUMA) servers with 192+ GB of RAM. We have been using Dell PowerEdge R630 with 48 logical processors and 192 GB (spec attached - purchased for under $10,000 USD). For best import performance, use SkylineRunner command-line interface with --import-process-count=12 (or similar). Be sure to run tests. Mileage may vary depending on the import file format and disk drive type and speed.

With a large server like this, make sure the power profile is configured for "maximum performance", both in Windows and UEFI/BIOS. (Check Power Options and make sure this is not set to "Balanced", but "High performance" and check with your IT about BIOS settings.)



Parallel Import Performance


Attached to this page you will find a thorough study of how Skyline scales importing large scale DIA data with parallel file import of various file types on either a standard Intel i7 comptuer with 16 GB of RAM versus a Dell PowerEdge with 48 logical processors 196 GB of RAM, using either multiple threads or multiple processes.

General findings include:

  • Multiple process import can scale past mutiple threads in the same process (which we think is related to garbage collection)
  • Only multi-process import can take advantage of the true potential of a NUMA system with 24+ logical cores
  • The difference is much less pronounce on an i7 an may not be worth the effort to go multi-process
  • Many formats pay only a percentage increment for spinning disk versus SSD
  • The mz5 format, otherwise the fastest format to import, has serious problems scaling with parallel file import on a spinning drive

At the time of this writing, only the Skyline command-line interface (presented by SkylineRunner or SkylineCmd) can take advantage of multi-process import by using the --import-process-count argument.




Vendor-Specific Instrument Tuning Parameters


As of release 3.5, Skyline's small molecule support includes the ability to explicitly set many vendor-specific instrument tuning parameters on a per-precursor basis.

The "Insert Transition List" dialog for small molecules now has columns for importing various vendor-specific values such as "S-Lens", "Cone Voltage", "Declustering Potential" and "Compensation Voltage", along with the previously implemented ability to explicitly set "Collision Energy", "Retention Time" "Retention Time Window", "Drift Time", and "Drift Time High Energy Offset". These values can also be modified in the Document Grid.

These values can also be modified in the document grid for peptides (formerly this was only possible for small molecules).

By default S-Lens values are not written: a new checkbox in the Export Method dialog enables this for appropriate Thermo outputs. On the commandline side, there is a new argument "exp-use-s-lens" for this.




Support for Bruker TOF Instruments


Skyline v2.1 introduces fully integrated support for Bruker micrOTOF-Q and maXis series instruments.  The Skyline support for working with full-scan mass spectra has been extended to Bruker TOF instruments, and data acquired with them in several modes:

  • MS1 Filtering - chromatogram extraction from MS1 scans in data dependent acquisition (DDA) experiments
  • Targeted MS/MS (PRM) - chromatogram extraction from MS/MS scans in pseudo-SRM experiments
  • Data Independent Acquisition (DIA) - chromatogram extraction from MS/MS scans acquired in various isolation schemes
    • Consecutive wide windows
    • All Ions - alternating low energy and high energy scans of the entire instrument range

For more information on working with Skyline and Bruker TOF instruments, consult the following resources:

  • HUPO 2012 Bruker Lunch Seminar [PowerPoint][PDF]
  • Targeted Proteomics with Bruker TOF Instruments tutorial [PDF]

The following supporting files may also be useful:

  • Skyline template documents for Bruker TOF data analysis [ZIP]
  • Script for adding retention times to MGF files for peptide searches [Script]



SCIEX Instrument Settings


Attached to this page you will find Skyline settings files created by SCIEX as helpful defaults for the QTRAP and TripleTOF instruments.

To load these settings files into Skyline, perform the following steps:

  • On the Settings menu, click Import.
  • Select one of the .skys files.
  • Click the Open button.

This will add a new menu item to the Skyline Settings menu, either QQQ_QTRAP_Environment or TripleTOF_Environment depending on which file you imported.  To change the settings on your current document, simply choose one of these menu items.  This will change the document settings to the defaults that AB SCIEX has created for their instruments.

 

Note that if you employ explicit tuning parameters such as Explicit Collision Energy or Explicit Declustering Potential these must be absolute values (i.e. positive numbers). When writing transition lists for negative ion mode operation, Skyline will automatically express them as negative values.




Export SRM Methods for a Thermo LTQ


You may know that Skyline documents can be exported to MRM/SRM transition lists for all of the major triple quadrupole instruments available today.  You may even know that Skyline documents can be exported directly to native methods for some of these instruments.  But, Skyline can also export SRM method files for the Thermo-Scientific LTQ.

An ion trap instrument like the LTQ may not have the sensitivity of a triple quadrupole, but you can still use one for targeted proteomics, and you can use SRM on the LTQ as a quality control measure for your liquid chromatography.

While you can export an existing Skyline document to a native LTQ method for SRM, you should be aware of a couple settings before you do.  To prepare your document for use with the LTQ, perform the following steps:

  • On the Settings menu, click Transition Settings.
  • Click the Instrument tab.
  • Check Dynamic min product m/z.
  • Enter the correct value (e.g. 2000) for your instrument into the Max m/z field.
  • Click the OK button.

The first setting will restrict the product m/z values Skyline will allow to being greater than a dynamic minimum, based on the precursor m/z, consistent with the limits the LTQ imposes.  The second setting will restrict both the precursor and product m/z values Skyline allows to be consistent with what your LTQ is calibrated to allow.

If you have done this on an existing document, you should probably review your transitions to be sure Skyline has not removed anything important.  Small product ions may no longer be measurable on the LTQ, which could cause some precursors to contain fewer transitions than you want for your experiment.

If this is a new document, you can now enter the peptides you are interested in targeting as you would normally, understanding that some smaller product ions that you would normally see will no longer be available in the Skyline user interface.

When you are ready to export a LTQ method file for your Skyline document, you must transfer your Skyline document to the instrument control computer for your LTQ instrument, where you will also need to have Skyline installed.  If you are using a complex document involving spectral libraries, you may want to consider using the Share command on the File menu, as described in the tip on Sharing Skyline Documents in Manuscripts.

Once you have your Skyline document open on the LTQ instrument control computer, you are ready to export it to a native LTQ method or .meth file.  To do this, preform the following steps:

  • On the File menu, choose Export, and click Method.
  • Choose 'Thermo LTQ' from the Instrument type list.
  • Click the Browse button beside the Template file field.
  • Browse to a .meth file you will use as a template for all settings other than the m/z values to monitor.
  • Click the Open button in the Method Template form.
  • Choose options in the rest of the Export Method form as you would for exporting a transition list or a TSQ native method.
  • Click the OK button.
  • Enter a name for your method, or root name if creating multiple methods.
  • Click the Save button.
This will create a LTQ method or multiple methods which you can use to make SRM measurements on your LTQ.  Once these are complete, you can import the resulting Thermo .RAW files as you would .RAW files from a TSQ triple quadrupole instrument.

Using SRM for Liquid Chromotography Quality Control on the LTQ

Issues with chromatography can easily go unnoticed on systems performing predominantly shotgun data dependent analysis (DDA).  They can, however, still greatly effect performance, especially if you are hoping to use tools that analyze MS1 scan data for quantification and feature detection.  At the MacCoss lab, we are using SRM methods generated with Skyline to monitor LTQ system performance.  Every tenth run on our LTQ instruments, we inject a known standard mix and measure its abundant peptides using SRM.  We find that measured retention times and peak shapes of known peptides give us increased visibility into system performance of the LTQ.

At present we are injecting the "6 Bovine Tryptic Digest Equal Molar Mix PTD/00001/63" from Michrom Bioresources, Inc., running SRM methods generated with this Skyline document:

Bovine_Mix_QC.sky

Below are examples of Skyline displaying both failing and passing runs on our LTQ Velos. Each QC replicate displayed in Skyline was taken as every tenth injection with the other 9 injections used for normal shotgun MS/MS measurement.

Failing:
In the QC runs shown below, chromatography issues first appear between runs 9 and 12. By QC13, the system is clearly not functioning acceptably.

Passing: In the 33 QC runs shown below, both a retention time drift of about 2 minutes and decreasing intensity are visible, but measurements remain within an acceptable range throughout.




Integration with Other Tools


The Skyline project has implemented integration with many tools and instrument platforms.  Skyline supports building spectral libraries from the outputs of nearly 20 different peptide spectrum matching pipelines.  It exports methods to and imports data from the instruments of 6 different vendors.  And, Skyline integrates with a number of external tools and the Panorama targeted proteomics knowledge base.

Here are two brief tutorials describing how Skyline also integrates with other chromatography-based quantitative tools and information they may produce:

Importing Integration Boundaries from Other Tools
This tutorial covers Skyline support for importing the start and end integration times determined for peptide elution by tools other than Skyline.  You can use this feature to benchmark or visualize the performance of other tools, or simply to incorporate their results into a Skyline-based workflow.

Importing Assay Libraries
Several tools have begun to use enhanced transition lists (with added relative product ion abundance and normalized retention times - iRTs) called "assay libraries".  To better support this format, Skyline will now suggest creating an iRT calculator and a minimal spectral library during transition list import when these extra columns are detected.  Learn what to expect and what to watch out for when using this feature. 




How Skyline Builds Spectral Libraries


Skyline builds spectral libraries using a separate program called BiblioSpec, which has two main components. BlibBuild is called to build the redundant library, which is then filtered by BlibFilter to create the non-redundant library. The BlibBuild page contains information on the various search engines that are supported, along with information about their respective file formats and the scores used with the cut-off value specified in Skyline.

BlibFilter chooses the best spectrum within a group by simply using the one with the best score. If there are multiple spectra tied for the best score, the one with the highest TIC is selected. In the past, BlibFilter chose the spectrum with the highest average dot product when compared to all other spectra within the same group, but this method occasionally produced poor results. A similar method, computing a consensus spectrum and its dot product against the related spectra, also produced inferior results as it sometimes resulted in high-noise spectra being chosen.

Skyline with BiblioSpec supports building libraries from the following peptide spectrum matching pipeline outputs:

Database searchPeptide ID file extensionSpectrum file extension
*RAW includes vendor formats like RAW, WIFF, .D, etc.
Score UsedNotes
Generic SSL.ssl score columnA generic format for encoding spectrum library entries.
ByOnic.mzid.MGF, .mzXML, .mzMLAbsLogProb 
Comet/SEQUEST/Percolator.perc.xml, .sqt.cms2, .ms2, .mzXMLq-valuePercolator v1.17 does not include sequence modification information therefore the .sqt file from the SEQUEST search must be present in the same directory, the directory containing the cms2/ms2 spectrum files, or the current working directory.
DIA-NN.speclib noneNo separate spectrum file. In the current implementation, no score is imported from the library, so all spectra are imported.
IDPicker.idpXML.mzXML, .mzMLFDRThe name(s) of the spectrum file(s) are given in the .idpXML file.
MS Amanda.pep.xml, .pepXML.mzML, .mzXML, .MGF, RAW*q-value 
MSFragger.pep.xml, .pepXML.mzML, .mzXML, .MGF, RAW*q-value 
MSGF+.mzid, .pepXML.mzML, .mzXML, .MGF, RAW*expectation value 
Mascot.dat expectation valueNo separate spectrum file.
MaxQuant Andromedamsms.txt + evidence.txt + mqpar.xml + modifications.xml.mzML, .mzXML, .MGF, RAW*PEPIt is possible to use peaks embedded in the msms.txt, but external spectra files are preferred because the embedded peaks are charge deconvoluted. mqpar.xml must be located in the grandparent, parent, or same directory. A custom modifications.xml or modification.xml can be placed in the same directory as the search results (or specified using the -x option).
Morpheus.pep.xml, .pepXML.mzXML, .mzMLq-valueThe names of the .mzXML files are given in the .pep.xml file and may be in the parent or grandparent directory. Spectra are looked up by index, which is calculated using (scan number - 1).
OMSSA.pep.xml, .pepXML.mzXML, .mzMLexpectation valueThe names of the .mzXML files are given in the .pep.xml file and may be in the parent or grandparent directory.
OpenSWATH.tsv m_score columnNo separate spectrum file.
PEAKS DB.pep.xml, .pepXML.mzXML, .mzMLconfidence scoreThe names of the .mzXML files are given in the .pep.xml file and may be in the parent or grandparent directory.
PLGS MSefinal_fragment.csv score columnThere need not be a . before 'final_fragment'..
PRIDE.pride.xml variousNo separate spectrum file.
PeptideProphet/iProphet.pep.xml, .pepXML.mzML, .mzXML, .MGF, RAW*probability scoreThe names of the .mzXML files are given in the .pep.xml file and may be in the parent or grandparent directory.
PeptideShaker.mzid.MGFconfidence score
Protein Pilot.group.xml confidence scoreNo separate spectrum file.
Protein Prospector.pep.xml, .pepXML.mzML, .mzXML, .MGF, RAW*expectation value 
Proteome Discoverer.msf, .pdResult q-valueNo separate spectrum file. Libraries cannot be built from databases that do not contain q-values, unless a cutoff score of 0 is explicitly specified.
Proxl XML.proxl.xml.mzML, .mzXML, .MGF, RAW*q-value
Scaffold.mzid.MGF, .mzXML, .mzMLpeptide probability 
Spectronaut.csv noneSpectronaut Assay Library export. No separate spectrum file.
Spectrum Mill.pep.xml, .pepXML.mzXML, .mzMLexpectation valueThe names of the .mzXML files are given in the .pep.xml file and may be in the parent or grandparent directory.
X! Tandem.xtan.xml expectation valueNo separate spectrum file.

 

Importing Existing Spectral Libraries

Skyline can also directly read existing spectral libraries (without using BlibBuild) including:

  • SpectraST (.sptxt) 
  • theGPM  X! Hunter (.hlf) 
  • Shimadzu (.mlb)
  • Golm Metabolome Database (.msp)
  • NIST (.msp)

Working with NIST files

If your library contains spectra for multiple instruments and conditions (e.g. various CE values) it is important to use the NIST-supplied filtering tools to produce a subset of spectra appropriate to your experimental conditions. Each molecule+adduct (or peptide+charge) pair can appear in a .blib file only once, and without thoughtful filtering you will almost certainly produce a .msp file that can't be used by Skyline because it contains more than one instance of a molecule+adduct (or peptide+charge) pair.




ID Annotations Missing with Mascot Search Results


Skyline supports several workflows where the retention time of peptide search identified MS/MS spectra are used to help it pick chromatogram peaks, and for subsequent visual inspection.  The most visible effect of when this extra information is present and usable by Skyline is the addition of ID annotations to the chromatogram graphs, as shown below:

If you build a spectral library or use the Import Peptide Search wizard to import Mascot search results for use with full-scan chromatogram extraction, and find that you do not see ID annotations in your chromatograms as you would expect, the problem most likely originates with the MGF converter you used to create MGF files as input to Mascot.

For Skyline to be able to place an identified spectrum on an extracted chromatogram, it needs two things, beyond the peptide identification itself:

  1. A spectrum source file name that Skyline can match with the data file used to extract chromatograms.
  2. A retention time at which the spectrum was measured.

The spectrum source file name does not need to match exactly with the file specified in the Import Results form.  Skyline uses base name matching, which counts all of the following files as matching:

  • spectrum_source.raw
  • spectrum_source.mzXML
  • spectrum_source.c.mzXML
  • spectrum_source.ms2
  • spectrum_source.mzML

Note also that Skyline completely ignores any path information included with the spectrum source file name. Many converters will include a full path, but this is not necessary, and Skyline will match chromatogram data imported from any path, as long as the file basenames match.

The first place to look for clues on contents of any library is the Skyline Spectral Library Explorer (View > Spectral Libraries).  A library built from search results that contain the necessary information will look like this:

If you click the button beside the Library drop down list, Skyline will display the Library Details form with a list of the spectrum source files from which there are identified spectra in the library:

The most common issue you will see with a Mascot DAT file is that it does not contain spectrum source file information in a format that Skyline can understand.  That format can be traced back to the TITLE lines in your original MGF file.  Thanks to a lack of standardization in this area, a long stream of bug reports has lead to Skyline handling a number of different TITLE line formats, but the most flexible and robust format are:

TITLE=...File: "path/to/file.raw"...

or slightly less robust:

TITLE=...File: path/to/file.raw ...
TITLE=...[path/to/file.raw]

Since the first does not allow spaces in the path, and the second does not allow brackets in the path.  Note again that the path information will be ignored by Skyline in matching with imported chromatogram files, though characters in the path can have a negative impact on parsing of some formats (e.g. spaces in format that relies on a space as a terminal character).

The retention times are provided by RTINSECONDS lines in the MGF like:

RTINSECONDS=3006.0281

Problems in either of these can cause issues that show up like the following Spectral Library Explorer figures:

Issue 1: The TITLE line in the MGF file did not contain a recognizable format (described above) from which the spectrum source file can be parsed, causing the DAT file name to be used instead.  If your DAT file contains the search results for a single file, this can be corrected by simply renaming the DAT file to have the same base name as the data file you will import for chromatogram extraction (e.g. spectrum_source.dat).

Issue 2: The RTINSECONDS line in the MGF file was missing, causing the spectrum RT value to be set to zero.

Issue 3: A time outside the gradient length is shown.  Something has gone wrong with the library builder parsing this file.  You should report something like this to the Skyline team.

Issue 4: Every spectrum has a different source file not representative of files on disk.  Something has gone wrong with the library builder parsing this file.  You should report something like this to the Skyline team.

If you run into any problems like this, we always recommend installing ProteoWizard and using MSConvertGUI to create your MGF files, as shown below:

Note that you must make sure the TPP compatibility check box is checked.

If the MGF converter you used comes from an instrument vendor or professional software company, and you want help communicating with them what is required for full integration with a workflow that includes Skyline, either point them to this page, or post your issue to the Skyline support board.




Share Skyline Documents in Manuscripts


Skyline documents provide the ideal way to share targeted proteomics methods and results as supplementary material in your manuscripts.

Skyline has the following advantages that are not available in any other targeted proteomics software:
  • Open source
  • Freely available and easy to install
  • Vendor-neutral platform for targeted mass spectroscopy investigations of both proteomic and small-molecule data
  • Perform analysis of mass spectrometry data from a range of acquisition techniques such as selected reaction monitoring (SRM), data-dependent acquisition (DDA), parallel reaction monitoring (PRM), and data-independent acquisition (DIA)
    • Support for SRM instruments from Agilent, SCIEX, Shimadzu, Thermo-Scientific, and Waters
    • Support for full-scan instruments from: Agilent, Bruker, SCIEX, Thermo-Scientific and Waters
  • Human readable XML document format
  • Compact, high-performance, easily shared data cache file format

Once you have created a Skyline document (.sky) and its companion data cache file (.skyd), your entire method and acquired results can be easily shared with other researchers. You are guaranteed that others will have freely available and rich access to your method design and results data.
To create a sharable ZIP file that includes:
  • Skyline document (.sky)
  • Skyline data cache file (.skyd)
  • Skyline display information (.sky.view)
  • Either all used spectral libraries or the fraction used by the document (.blib & .redundant.blib)
  • The backgound proteome file (.protdb - optional)

Simply perform the following steps in Skyline:
  • On the File menu, click Share.
  • If the document uses spectral libraries or a background proteome:
    • Click the Minimize libraries radio button to share only the library spectra used in your document.
    • Click the Store everything radio button to share the libraries and background proteome files as they exist on your system
  • Enter the file name of your choice in the File name field (or accept the default).
  • Click the Save button.
You now have a compact file that can be shared publicly or upon request with any manuscript in which your methods and data are included.

Your readers will have open access to:
  • View your methods and data in Skyline's rich visual environment
  • Export transition lists or methods for their own instruments
  • Export custom reports for deeper analysis of your data


You can also share the report template(s) you found most useful in analyzing your data by doing the following:
  • On the Settings menu, choose Document Settings, and click the Reports tab.
  • Check the checkboxes beside the names of the reports you wish to share.
  • Save the document.
This will result in the selected reports getting embedded in the .sky XML file. When the file is opened on another computer the reports will automatically get imported making it easy for readers to repeat your analysis on the systems in their labs, with their own samples.

Sharing Skyline results on Panorama Public

Sharing Skyline documents associated with manuscripts is made easier with Panorama Public, a centralized, community resource of published results processed with Skyline. Panorama Public facilitates viewing, sharing, and disseminating results contained in Skyline documents via a web-browser. In addition to viewing results in the Panorama interface, Skyline documents published to Panorama Public can be downloaded in their original form and opened with Skyline for an in-depth exploration.

Submitting Skyline results to Panorama Public involves:
  • Getting a free project for your lab on PanoramaWeb, which is a server repository that is used by several laboratories and organizations to store their Skyline-processed data
    • Click here to request a new project
  • Uploading and organizing Skyline documents within sub-folders of a project on PanoramaWeb
  • Submitting data to Panorama Public
    • Click here for step-by-step documentation
    • Click here for a more detailed tutorial

Data submitted to Panorama Public can be private initially while the manuscript is under review. A reviewer account is provided to the submitter. When the manuscript is accepted for publication data is made public.

Panorama Public is a member of the ProteomeXchange Consortium which is a group of repositories dedicated to the standardized submission and dissemination of proteomics data worldwide. Proteomics data submitted to Panorama Public that fulfills all of the ProteomeXchange requirements is assigned a unique ProteomeXchange accession that can be included in the manuscript. Published data associated with a ProteomeXchange ID is made available to a wider research community via the ProteomeXchange portal and can be searched on the portal with the unique PXD accession number assigned to the data.

Skyline and Panorama Public help you give the proteomics and small molecule research cummunity full, open access to your methods and results.



Sharing MS/MS Spectra with Manuscripts


If you are looking for a MS/MS spectrum viewer, you may not be familiar with Skyline, a tool developed primarily to aid targeted proteomics investigation.  Skyline does, however, provide features that make it ideal for sharing MS/MS spectra with manuscripts before and after publication.  Skyline displays fully annotated spectra for peptides with post translational modifications (PTMs) and neutral losses extremely quickly, and the Skyline software itself is freely available and easy to install. [Install Now]

If you already have a Skyline document that was submitted as part of a manuscript follow the steps below to use Skyline to view these spectra:

  • On the File menu, click Open (ctrl-O).
  • Select the shared file you are working with (usually .sky.zip).
  • Click Open.

Once the file is open in Skyline, it should look something like this:

If you do not see the MS/MS spectrum graph:

  • On the View menu, click MS/MS Spectra.

If you want to see different precursor charge states for the peptides in the document:

  • On the Edit menu, choose Expand All and click Peptides.

Select peptides or precursors in the Peptide View on the left to see the corresponding MS/MS spectrum.

For PTMs in the Peptide View, any modified amino acid is bold and underlined.

If you hover over a protein name, the positions of the peptides it contains are highlighted in bold colored text.  If a peptide is selected in the Peptide View, it is highlighted in red.

 If a peptide of interest contains post translational modifications (as in this case Ser-348 phosphorylation) you can see the modified amino acid bold and underlined in the Peptide view.  You can also hover over the peptide and Skyline will present more information in a tip, including the delta-mass of each modification specified in brackets in a field labeled “Modified”.

The MS/MS spectrum is interactive and one can zoom into the spectrum, using the mouse scroll wheel or by clicking and dragging a box around a region of interest, to see further fragmentation details.

In the above case of MS/MS for GSLAS348LDSLR [344, 353], zooming in clearly shows that Ser-348 is phoshorylated, and that there is no site ambiguity as the y5 ion and the y6/y6-98 ions clearly determine the position of the phospho group on Ser-348.

If there is phosphorylation site ambiguity, and the PTM site is indistinguishable, Skyline can be used to simulate both peptide isoforms and to easily indicate site ambiguity:

Such as the peptide

R.GEPNVSYICSR.Y [272, 282], phosphorylation simulated at Ser-277  

and the isoform

R.GEPNVSYICSR.Y [272, 282], phosphorylation simulated at Ser-281

In the Skyline document shown below, both isoforms have a pink triangle in the upper right corner of the peptide label.  This triangle indicates an annotation on the peptide.

To view the peptide annotation, right-click on the peptide sequence in the Peptide View and click Edit Node to view a form like the one displayed below.  (In version 1.2 and later, these annotations are shown in the peptide details tip mentioned above, and also by themselves if you hover the mouse over the colored triangle.)

Skyline Custom Annotation can be used to indicate the site ambiguity as demonstrated above with the “TRUE/FALSE” check mark within the peptide note.  These Annotations can easily be exported into custom Skyline reports (csv files).  For more information on annotations and reports, consult the Skyline Custom Reports & Results Grid tutorial.

Publishing a Skyline document for MS/MS spectrum viewing as part of manuscript submission allows the reader to interactively view MS/MS spectra.  Skyline can help with assessment of site ambiguity and allow you to indicate, using custom annotation, cases where site ambiguity of PTMs exists.

These Skyline spectral libraries can be further used to design targeted assays and may provide a valuable resource for researchers interested in a certain data set.

For manuscript submission, Skyline spectral libraries can easily be generated from many common peptide identification search engine outputs, for further details see the Skyline Spectral Library Explorer tutorial. 




Miscellaneous





Skyline Batch


  Skyline Batch is an application that automates a common Skyline workflow for batch processing Skyline documents. It interacts with Skyline through the command-line, allowing it to import data into a template document, export reports, and run R scripts on those reports without bringing up the Skyline user interface.

 

Install Skyline Batch for Skyline 20.2 or later, or Skyline-daily (20.2.1 or later)

Skyline Batch Documentation

 

 

Skyline Batch Webinar

A hands-on demonstration displaying the depth of Skyline Batch as well as new features:

Webinar 20: Using Skyline Batch for Large-Scale DIA

 

Skyline Batch Tutorials

Learn how to use Skyline Batch by completing the supplementary tutorials on the Webinar 14 and 15 pages:

Webinar 14: Large Scale DIA with Skyline

Webinar 15: Optimizing Large Scale DIA with Skyline

 

 

Skyline Batch Release Notes

 

Skyline Batch 21.1.0.187 (July 6th, 2021)

  • Skyline template files, annotation files, data files, and R scripts can now be downloaded from Panorama
  • New download data files dialog that includes an interactive list of the files to be downloaded
  • Improved Skyline Batch configuration files that are more easily readable in a text editor
  • Updated run button options

 

Skyline Batch 21.1.0.146 (May 26th, 2021)

  • Added a "download files only" run option
  • Allow waiting configurations to be unchecked and removed from the current batch run
  • Log improvements
  • Data download bug fixes

 

Skyline Batch 20.2.0.475 (Apr. 20th, 2021)

  • Can download data files from an FTP server
  • Added support for different number formats

 

Skyline Batch 20.2.0.464 (Apr. 9th, 2021)

  • Import configurations by double-clicking a Skyline Batch Configuration file
  • No longer requires a Skyline report file for reports that already exist in the template document
  • Improved file detection for sharing configurations across computers 

 

Skyline Batch 20.2.0.453 (Mar. 29th, 2021)

  • New option for Skyline file refinement
  • Supports using refined files as templates for other configurations
  • Added ability to import annotations
  • Bug fixes for finding R installations, logging, and more

 

Skyline Batch 20.2.0.398 (Feb. 2nd, 2021)

  • Runs multiple Skyline workflows sequentially
  • Displays log of current run
  • Allows different configurations to use different Skyline installations
  • Supports running R scripts with any version of R

 

 




Skyline File Types and Extensions


Here is a complete list of Skyline file types:

  • .sky - the main Skyline document file
  • .sky.view - contains state information about the Skyline UI when the .sky file was last saved, e.g. selection and window layout - can be deleted
  • .skyd - contains all the chromatograms and the complete set of peak statistics (generally 10 per chromatogram) considered by Skyline
  • .skyl - the Skyline audit log file
  • .blib - a Skyline native spectral library
  • .slc - a "spectral library cache" created to improve initial spectral library load performance - can be deleted and Skyline will simply recreate it
  • .irtdb - a Skyline iRT library file
  • .optdb - a Skyline optimization library for CE and CoV optimization values
  • .protdb - a background proteome file
  • .imsdb - and ion mobility library (coming in 20.2) which stores ion mobility and CCS values
  • .midas - a spectral library file for spectra from SCIEX MIDAS runs

External library types:

  • .hlf - X! Hunter spectral library from theGPM
  • .sptxt - SpectraST spectral library from the TPP
  • .msp - NIST spectral library

But don't try to understand all of the above just to share a complete Skyline document/project with others, instead use File > Share or Upload to Panorama to create a:

  • .sky.zip - a compressed ZIP archive which contains the full set of files required to share your document/project

Exported files not associated with the .sky file:

  • .skys - a Skyline settings file which can be imported into a menu item on the Skyline Settings menu
  • .skyr - a Skyline report template file which can be imported back into Skyline to add report templates to the available set
  • .skyp - a new Skyline "pointer" file that can be downloaded from Panorama very quickly and will then initiate a full download inside Skyline when opened



Waters SONAR Calibration


Waters SONAR support has recently been improved in Skyline. SONAR users should consult this information provided by Waters:  https://support.waters.com/KB_Inf/MassLynx/WKB202040_How_to_create_post-acquisition_a_SONAR_calibration_file




Audit Logging


(This tip applies to Skyline-Daily 4.1.1.18257 and later.)

When enabled, the audit log will keep track of all changes that are made to the current document. The audit log is stored as a separate file (.skyl), alongside with the skyline document.

The audit log can be accessed from the View menu. The audit log is displayed in a grid, similar to the document grid. In the top right corner audit logging can be enabled or disabled.

For new documents, audit logging is enabled by default.

Reasons to enable Audit Logging

•Reproducibility: The audit log makes it easy to see what changes were made to a document and can be used to reproduce a document step-by-step. 
•Collaboration: If multiple people are working on the same document it can be helpful to have a record of what each person has done to the document. 
•Troubleshooting: If the user encounters an error in Skyline, the audit log can be helpful for the Skyline team to diagnose and fix the issue.

 

Full details can be found here (PDF).




Crosslinking in Skyline 21.1


Support for crosslinked peptides was first added to Skyline version 20.2.

Skyline 21.1 improved this feature by making it much easier to link more than two peptides together.




New in Skyline 4.1


Attached are a collection of slides created by the developers as they added new features in Skyline 4.1 which required a bit of explanation:

  • Small molecule spectral libraries, improved adducts, and identifier (InChiKey, InChi, CAS, and HMDB)
  • Document Grid and Live Report pivot and layout support
  • Group comparison volcano plot with formatting
  • Peak Area CV histogram plots
  • Quantitative property for transitions
  • Points across the peak visualization in chromatogram plots



How to Display Multiple Peptides


Skyline allows you to compare chromatograms of different peptides by selecting them in the Targets  panel shown by default on the left side of the Skyline window.

For example, to see all the peptides belonging to a particular protein, click on the protein name in the Targets panel:

Skyline generates a color for each peptide based on the peptide sequence and modifications.  This provides a quick way to identify the matching chromatogram in the graph.  A peptide will always have the same color, even in different Skyline documents, unless there is another peptide within the same protein that generates the same color.  That doesn’t happen too often, but when it does, Skyline picks one of the conflicting peptides and assigns it a new color that is easier to differentiate.

Color swatches are shown in the Targets panel next to only those peptides which are shown in the graph.  In the example above, only the peptides under the selected protein are shown in the graph.

The peptides are also labeled in the graph with a unique abbreviation.  If the first three letters of the peptide’s name are unique (among the peptides being graphed), then only three letters will be used in the abbreviation.  If the first three and last three letters together are unique, the abbreviation will use those (see ASL…KGK in the example above).  More complicated abbreviation schemes are used if the first and last three letters are not unique.  Note that a peptide’s abbreviation can change depending on what other peptides are being displayed at the same time.

Graphing peptide subsets

The Targets panel allows you to select any subset of peptides you want.  You can select just a few peptides (from one protein, or across different proteins) by clicking on the first, and then holding the CTRL key down while clicking on additional peptides.  You can toggle a peptide by clicking on it multiple times with the CTRL key depressed.

You can select individual peptides by clicking on their names, or you can select all the peptides belonging to a protein by clicking on the protein name.

 

 

All peptides

To see every peptide in the document graphed, click somewhere in the Targets panel to transfer focus there, then type CTRL-A (or choose Select All from the Edit menu):

Note that this can take some time to display if your document contains a large number of peptides.

Displaying all the peptides will produce a graph that looks similar to the progress displayed during data import:

But you can see differences between this graph and the one above.  Peptide colors will usually match, but occasionally they don’t if a different color is needed to disambiguate two peptides in the same protein.  Peak values can also differ, because different summation criteria are used during import than later when more processing has been done on the raw data.




Ion Mobility Separation (IMS) Data


Skyline supports IMS data for Waters, Agilent, Thermo (FAIMS) and Bruker instruments.  By specifying the ion mobility for each precursor ion of interest you can tell Skyline to ignore scans that might contribute noise, and thus improve the quality of extracted chromatograms. The Ion Mobility Spectrum Filtering tutorial provides examples and more detail.

Ion mobility values may be specified in Ion Mobility libraries, or defined explicitly in transition list imports, and may also be found in spectral libraries (for the latter, make sure to check the "Use spectral library ion mobility values when present" box in the Ion Mobility tab of the Transition Settings dialog). The order of precedence is: explicit values, Ion Mobility Library values, Spectral Library values.

You will notice that an ion mobility is commonly expressed as a Collision Cross Section (CCS) value and an ion mobility value. It's important to understand that the CCS value takes priority: different raw data files may contain different CCS->mobility calibrations, so the actual ion mobility filter value for a chromatogram extraction is always derived from the CCS value when available. Thus, if you want to experiment with adjusting ion mobility values for chromatogram extraction, it's import to either adjust CCS rather than ion mobility, or to clear the CCS setting so that your adjusted ion mobility value is the one that gets used. 

To add or modify an ion mobility library, use the Settings|Transition Settings menu item and select the Ion Mobility tab, then use the "Ion Mobility Library" drop down menu to bring up the Ion Mobility Library editor.  

The easiest way to set up an ion mobility library is to start with a Skyline document with imported results, then use the "Use Results" button in the Ion Mobility Library editor.  This simply scans the existing imported results and determines the ion mobility value of the scan containing the most intense peak.  Once you have that, you can reimport the data and Skyline can ignore scans at the proper retention time but wrong ion mobility.

There is a risk, of course, that the most intense peak at a given retention time isn't actually that of the precursor you are interested in, in which case you will be making the noise situation worse instead of better.  The ideal way to use this training feature is with simple training sets that elute one precursor at a time.  If you do not have that capability then you should go through and verify the ion mobility selections manually using the Full Scan chromatogram viewer's intensity heat map of mz vs ion mobility.

You can also set explicit ion mobility values for small molecule precursors using the right-click menu in the Targets window. This can also be done in the Document Grid, so it's possible for peptide precursors as well.




Skyline Source Code


The Skyline project is developed in open source, under Apache 2.0 License, though released under a modified Apache 2.0 License, due to the inclusion of third party libraries with licensing restrictions.

The source code for Skyline is made available through the ProteoWizard GitHub Repository. The main Skyline project can be found under:

pwiz_tools/Skyline

If you are interested in working with the Skyline source code, follow the "How to build Skyline" instructions.




How to build Skyline


How to Build Skyline

Follow these steps to configure your PC to build Skyline:

 GitHub

The Skyline source code is part of the ProteoWizard project, and is hosted at GitHub.

  1. You will need a GitHub account 
  2. You will need to configure it to use two factor authentication.
    Don't go down any rabbit holes about SSH keys yet. See the next step for that.
  3. You will also need to set up an SSH key and add it to your GitHub account
    You can ignore the stuff about GitLab, it's GitHub we're interested in.
    In the step where you create the .ssh directory, you may have to use the windows command line "mkdir" rather than Windows Explorer (some systems don't like a folder name that starts with ".").

 

TortoiseGit

You can use this or any Git client you like, as long as it provides C:\Program Files\Git\cmd\git.exe - the Skyline team uses TortoiseGit and Git For Windows.

  1. Download from https://tortoisegit.org/download

  2. Just accept the defaults during the installation.

  3. If you don't already have a git.exe, let TortoiseGit help you download and install Git For Windows.

  4. If you're installing Git For Windows, just accept the defaults. If it asks you for your GitHub login, provide that if you have one, or tell it you'll do that later.

  5. It's recommended to edit your settings so that some commonly used operations are promoted to the main right click menu:
    Create Branch, Log, Diff, Check for modifications, Add, and Switch/checkout

  6. It's also recommended that you run this git command to set your CRLF defaults: "git config --global core.autocrlf true".  This gives you Windows-style line endings in your editor, but saves the standard Unix line endings on GitHub.

  7. If you're planning on making commits to the codebase, a ProteoWizard owner can grant access to the organization here

Visual Studio

Skyline requires Microsoft Visual Studio 2017 or 2019. The free Community Edition is sufficient, but ideally you would use Enterprise edition, as does the Skyline team. You can have multiple versions of Visual Studio on your computer, but the only officially supported versions are Visual Studio 2017 and 2019. When you install, select the options to enable both C++ and C#.
If you are using VS2017 you probably will need to download and install the .NET 4.7.2 SDK as well.

Anti-virus Exemptions

You will need to exclude the ProteoWizard source code tree from antivirus inspection. If you don't, Skyline's "AaantivirusTestExclusion" test will fail, and other tests will run inefficiently. How this is done depends on your choice of antivirus software. 

Mascot Parser

  1. Go to http://www.matrixscience.com/msparser_download.html to register with Matrix Science
  2. They'll send you an email, follow the instructions to download the latest for 64 bit windows. 
  3. Run (as administrator) the 64 bit self-extractor, extracting to "C:\Program Files\Matrix Science\Mascot Parser\"

Checking out the ProteoWizard source code with TortoiseGit

  1. Create a ‘Proteowizard’ folder somewhere (i.e. under I:\proj)
  2. Right-click in the folder and select Git Clone (if that's not there, you skipped TortoiseGit install)
  3. For "URL:" enter git@github.com:ProteoWizard/pwiz.git
  4. Check the "Load Putty Key" box, and enter the path to the .ppk file that you created earlier (it's in your .ssh directory).
  5. Click OK. 
  6. The first time you do this, you'll get a message from the Pageant progrem (part of Putty) asking for the keyphrase you gave when you created your .ppk file. You'll also get a security alert about an uncached key, respond "Yes".

To Build Skyline and ProteoWizard

This step builds the ProteoWizard core library used by Skyline to read mass spec data, as well as Skyline itself, and runs tests on both.  Once you've done this, as a Skyline developer you'll mostly work in the Visual Studio IDE.  If you need to work on the ProteoWizard core, it's back to the bjam-based build system (though you can follow the debugger from Skyline into the pwiz core, if pwiz is built with the "debug" option). 

In these instructions, <root> refers to that umbrella directory you set up earlier as an antivirus exclusion.

  1. In a command prompt window, change directory to the root of the project that you cloned from github
  2. Create a batch file named "b64.bat" in this directory by creating a new file text file with a single line like this:

    pwiz_tools\build-apps.bat 64 --i-agree-to-the-vendor-licenses toolset=msvc-14.1 %*

  3. If you are using Visual Studio 2019 rather than Visual Studion 2017, the toolset argument should be "msvc-14.2" instead of "msvc-14.1"
  4. Type b64.bat in the command-line.
  5. Skyline will build, along with ProteoWizard tools like msconvert and SeeMS. You'll see lots of Skyline windows flashing by as the tests are run.
For the quickest possible build (quick because it skips tests), create a batch file bs64.bat containing the line "call b64.bat pwiz_tools\Skyline//Skyline.exe" and use that instead.

Test and Begin Skyline Development

Note that the first time you open Skyline.sln, you are likely to be asked to download and install an update dotNet package - do that.

  1. In Windows Explorer navigate to <root>\proj\Proteowizard\pwiz\pwiz_tools\Skyline
  2. Double-click Skyline.sln
  3. Be sure that your build configuration (RELEASE x64) is set correctly.
  4. Make sure your test settings match your build configuration:
    Test > Test Settings > Select Test Settings File
    and browser for either TestSettings_x64.runsettings in the Skyline folder
  5. On the Tools menu, click Options, select Debugging, select General, and uncheck the 'Enable Just My Code (Managed only)' option.
  6. On the ReSharper menu, if you have one, click Options, under Tools, select Unit Testing, select Test Runner, and switch the the 'Shadow-copy assemblies being tested' option to 'None'.
  7. In the Test menu, choose Run and click All Tests in Solution
  8. Once all of the tests have passed, you are ready to explore the code and implement new features.



Documentation


Most of the existing Skyline user documentation can be found in the Videos, Tutorials and Tips sections.  Here, however, are a few documents which do not fit into those categories, but still provide useful information on advanced topics in using Skyline for targeted proteomics data analysis:

  • Skyline Command-Line Interface - Learn about SkylineRunner.exe and how you can use it to run certain Skyline operations from a command-line.
    NOTE: for the most current command-line documentation, run SkylineRunner.exe or SkylineCmd.exe without any command-line arguments.  The same information can be found in the Skyline user interface at Help > Documentation > Command Line.
  • Skyline External Tools Documentation - Learn how to integrate with Skyline statistical and bioinformatics tools you are developing.
  • Skyline Interactive Tools Documentation - Learn how to integrate with Skyline interactive tools written with .NET which can request data from Skyline and respond to document changes on the fly.



Users Meetings


Since 2012, the Skyline team has been holding an annual User Group Meeting the Sunday before the annual ASMS conference.  Made possible by the generosity of our vendor sponsors, the User Group Meeting has showcased the creative and innovative ways that Skyline has been used in mass spectrometry research.  

To view a recording from a talk during a past Skyline User Group Meeting, select from one of the years below and then chose a speaker.  The session recording (if available) and presentation slides will appear below the abstract for the talk. 

2020 - Online

2019 - Atlanta

2018 - San Diego

2017 - Indianapolis

2016 - San Antonio

2015 - St. Louis

2014 - Baltimore

2013 - Minneapolis

2012 - Vancouver




Publications


If you use Skyline in your experiments, please cite our Bioinformatics 2010 application note, or the more recent and comprehensive Pino, Mass Spectrometry Reviews 2017 paper, listed below.
If you use Skyline for small molecule research, please cite our Journal of Proteome Research 2020 paper, listed below.
If you use Skyline for calibrated quantification, please cite our Clinical Chemistry 2017 letter, listed below.
If you use Skyline MS1 filtering, please cite our Mollecular Cellular Proteomics 2012 paper, listed below.
If you use Skyline for collision energy optimization, please cite our Analytical Chemistry 2010 paper, listed below.

Please feel free to download the Skyline logo vector graphics and use them in your papers to illustrate your use of Skyline for data analysis.

Peer reviewed manuscripts:

  • MacLean, Bioinformatics 2010 paper (cited by 3,134)
    Skyline: An Open Source Document Editor for Creating and Analyzing Targeted Proteomics Experiments
    [abstract][pdf]
  • Pino, Mass Spectrometry Reviews 2017 paper (cited by 154)
    The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics
    [abstract][full-text]
  • Adams, Journal of Proteome Research 2020 paper (cited by 25)
    Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics
    [abstract][full-text]
  • Rohde, Bioinformatics 2020 paper
    Audit Logs to enforce document integrity in Skyline & Panorama
    [abstract][full-text]
  • MacLean, JASMS 2018 paper (cited by 24)
    Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions
    [abstract][pdf]
  • Henderson, Clinical Chemistry 2017 letter (cited by 26)
    Skyline Performs as Well as Vendor Software in the Quantitative Analysis of Serum 25-Hydroxy Vitamin D and Vitamin D Binding Globulin
    [abstract][full-text]
  • Bereman, Journal of Proteome Research 2016 paper (cited by 35)
    An Automated Pipeline to Monitor System Performance in Liquid Chromatography Tandem Mass Spectrometry Proteomic Experiments
    [article]
  • Sharma, Journal of Proteome Research 2014 paper (cited by 149)
    Panorama: A Targeted Proteomics Knowledge Base
    [article]
  • Sharma, Mollecular & Cellular Proteomics 2018 paper (cited by 81)
    Panorama Public: A public repository for quantitative data sets processed in Skyline
    [article]
  • Broudy, Killeen, Bioinformatics 2014 paper (cited by 33)
    A framework for installable external tools in Skyline
    [abstract]
  • Schilling, Analytical Chemistry 2015 paper (cited by 67)
    Multiplexed, Scheduled, High-Resolution Parallel Reaction Monitoring on a Full Scan QqTOF Instrument with Integrated Data-Dependent and Targeted Mass Spectrometric Workflows.
    [abstract]
  • Egertson, Nature Protocols 2015 paper (cited by 154)
    Multiplexed peptide analysis using data-independent acquisition and Skyline
    [abstract]
  • Abbatiello, Mollecular Cellular Proteomics 2015 paper (cited by 148)
    Large-scale inter-laboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma
    [abstract]
  • Egertson, Nature Methods 2013 paper (cited by 258)
    Multiplexed MS/MS for improved data-independent acquisition
    [abstract]
  • Abbatiello, Mollecular Cellular Proteomics 2013 paper (cited by 102)
    Design, Implementation, and Multi-Site Evaluation of a System Suitability Protocol for the Quantitative Assessment of Instrument Performance in LC-MRM-MS
    [abstract]
  • Schilling, Mollecular Cellular Proteomics 2012 paper (cited by 374)
    Platform independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in Skyline. Application to protein acetylation and phosphorylation
    [abstract]
  • Choi, Journal of Proteome Research 2017 paper (cited by 21)
    ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC-MS/MS Experiments.
    [abstract]
  • Sherrod, Journal of Proteome Research 2012 paper (cited by 68)
    Label-Free Quantitation of Protein Modifications by Pseudo-Selected Reaction Monitoring with Internal Reference Peptides
    [abstract]
  • Escher, Proteomics 2012 paper (cited by 415)
    Using iRT, a normalized retention time for more targeted measurement of peptides
    [abstract]
  • Bereman, Proteomics 2012 paper (cited by 100)
    The development of selected reaction monitoring methods for targeted proteomics via empirical refinement
    [abstract]
  • Stergachis, Nature Methods 2011 paper (cited by 126)
    Rapid empirical discovery of optimal peptides for targeted proteomics
    [abstract]
  • MacLean, Analytical Chemistry 2010 paper (cited by 231)
    Effect of Collision Energy Optimization on the Measurement of Peptides by Selected Reaction Monitoring (SRM) Mass Spectrometry
    [abstract]
  • Prakash, Journal of Proteome Research 2009 paper (cited by 167)
    Expediting the Development of Targeted SRM Assays: Using Data from Shotgun Proteomics to Automate Method Development
    [abstract]

Publications featuring Panorama:

  • PanoramaWeb Publications Page
    [link]

Presentations and posters:

  • MacLean, ASMS 2020 Presentation
    Skyline integrates the Prosit prediction server for proteome-wide DIA data analysis using on-demand fragment intensity and iRT prediction
    [pdf] [video]
  • Pratt, ... MacLean, ASMS 2020
    Skyline Support for Proteome-wide Data Analysis of Bruker timsTOF dia-PASEF Acquisition
    [pdf]
  • Rohde, ASBMB 2019, Poster
    Integration of the deep learning prediction tool Prosit into Skyline for high-accuracy, on-demand fragment intensity and iRT prediction 
    [pdf]
  • Rohde, Chupalov, ASMS 2019, Poster
    Audit Logs to enforce document integrity in Skyline and Panorama
    [pdf]
  • Pratt, ASMS 2019 Poster
    Metabolomic Profiling of Small Molecule Ion Mobility Assisted Data Independent Acquisition Data Using Skyline
    [pdf
  • Pratt, ASMS 2017 Poster
    Recent Advances in Skyline: Further Improvements in Small Molecule Targets and Ion Mobility
    [pdf
  • Pratt, ASMS 2015 Poster
    Recent Advances in Skyline: Small Molecule Targets and Ion Mobility Filtering
    [pdf]
  • Thompson, MSACL 2015 Poster
    Skyline for small molecules: a flexible tool for cross-platform LC-MS/MS method creation and data analysis for metabolomics
    [pdf]
  • MacLean, ASMS 2014 Presentation
    Rapid Processing of Large Scale Quantitative Proteomics Projects: Integration of Skyline with the CHORUS Cloud
    [pdf]
  • Amodei, ASMS 2014 Poster
    A multi-site, Skyline-based comparison of DIA peptide detection and statistical confidence tools
    [pdf]
  • MacLean, ASMS 2013 Poster
    Integration of mProphet chromatogram peak identification probability model into Skyline
    [pdf]
  • Amodei, ASMS 2013 Poster
    An Instrument-Independent Demultiplexing Method for Computationally Improving the Specificity of Data-Independent Acquisition
    [pdf]
  • Eckels, ASMS 2013 Poster
    Sharing targeted proteomics assays using Skyline and Panorama
    [pdf]
  • MacLean, ASMS 2012 Presentation
    Targeted Proteomics Quantitative Analysis of Data Independent Acquisition MS/MS in Skyline
    [pdf] [PowerPoint] [video]
  • Sharma, ASMS 2012 Poster
    Panorama: A private repository of targeted proteomics assays for Skyline
    [pdf]
  • Egertson, ASMS 2012 Poster
    Multiplexed Data Independent Acquisition for Comparative Proteomics
    [pdf]
  • MacLean, ASMS 2011 Poster
    Skyline: Targeted Proteomics with Extracted Ion Chromatograms from Full-Scan Mass Spectra
    [pdf]
  • Tomazela, ASMS 2011 Poster
    Developing system suitability criteria and evaluation methods for proteomics experiments
    [pdf]
  • MacLean, ASMS 2010 Presentation
    Skyline: Sharing SRM/MRM Method Creation and Results Analysis Across Laboratories and Instrument Platforms
    [pdf]
  • Tomazela, ASMS 2010 Poster
    Effect of Collision Energy Optimization on the Measurement of Peptides by Selected Reaction Monitoring (SRM) Mass Spectrometry
    [pdf]
  • MacLean, ASMS 2009 Poster
    Automated Creation and Refinement of Complex Scheduled SRM Methods for Targeted Proteomics
    [pdf]

Invited reviews:

  • US HUPO News 2011 TechTalk - Skyline: A Bridge Between Discovery and Targeted Proteomics
    [article]



ASMS 2012 WOA am MacLean Presentation


Watch the video recording of Brendan MacLean's ASMS 2012 presentation Targeted Proteomics Quantitative Analysis of Data Independent Acquisition MS/MS in Skyline




ASMS 2020 WOA am MacLean Presentation


Watch the video recording of Brendan MacLean's ASMS 2020 presentation Skyline integrates the Prosit prediction server for proteome-wide DIA data analysis using on-demand fragment intensity and iRT prediction
[slides]




Press


 

  • Journal of the American Society for Mass Spectrometry (Volume 27, Number 11) lead front page story about Michael MacCoss receiving the 2015 ASMS Biemann Award from his work in bioinformatics and software for "omics" researchers (Skyline and Panorama). 
    [html] [cover pdf]
  • NCI eProtein feature
    Viewing the Targeted Proteomics Horizon with Skyline
    [html]
  • Nature Methods chooses targeted proteomics as Method of the Year in 2012
    Targeted proteomics
    [html]
  • NCI eProtein feature
    Open Source Software Tool Skyline Reaches Key Agreement with Mass Spectrometer Vendors
    [html]
  • PROTEOMICS article
    Free computational resources for designing selected reaction monitoring transitions
    [abstract]
  • Q-MOP Symposium review
    Quantitative proteomics: A central technology for systems biology
    [html]
  • NCI eProtein spotlight
    Skyline: Building a Bigger Net for Targeted Proteomics
    [pdf]



Awards


2016

  • Mike wins HUPO award Professor Mike MacCoss awarded the HUPO Discovery in Proteomic Sciences Award for his developments in methodology and software for the quantitative analysis of complex protein mixtures. The focus of his lab is the development of high-throughput quantitative proteomic methods and their application to model organisms. To enable this research, Mike and his research team have developed a software program Skyline -- a free, openly available software package for the design and interpretation of targeted proteomics experiments -- which as had a remarkable impact and is widely adopted within the proteomics community. This has placed Mike as a leader in the field of quantitative proteomics. [pdf]

  • Brendan MacLean wins inaugural Gilbert S. Omenn Computational Proteomics Award - In 2016, US HUPO announced the Gilbert S. Omenn Award for computational proteomics and the first recipient was no other than the MacCoss Lab's own Skyline Principal Developer, Brendan MacLean. The Omenn award recognizes the specific achievements of scientists that have developed bioinformatics, computational, statistical methods and/or software used by the proteomics community.

2015

  • Dr. Mike MacCoss wins ASMS Biemann Award for 2015 Professor Michael MacCoss received the 2015 American Society for Mass Spectrometry (ASMS) Biemann Award, in part, from the creation of software for "omics" researchers.  In their award announcement, ASMS cited Mike's philosophy on making high quality, freely available software -- Skyline and Panorama -- and providing for their long term support. This has enables many others to greatly benefit and has advanced the field of proteomic sciences, ASMS stated. 
    [html]



License Agreement


ADDENDUM TO APACHE LICENSE

To the best of our ability we deliver this software to you under the Apache 2.0 License listed below (the source code is available in the ProteoWizard project).  This software does, however, depend on other software libraries which place further restrictions on its use and redistribution.  By accepting the license terms for this software, you agree to comply with the restrictions imposed on you by the license agreements of the software libraries on which it depends:

SCIEX WIFF File Reader Library
Agilent Mass Hunter Data Access Component Library
ALGLIB numerical analysis and data processing library
Bruker CompassXtract
Shimadzu QQQ Data Reader Library
Thermo-Scientific MSFileReader Library
Waters Raw Data Access Component Library
Mascot Parser
 
NOTE:  If you do not plan to redistribute this software yourself, then you are the "end-user" in the above agreements.

 

Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
 

TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION

1. Definitions.

"License" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document.

"Licensor" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License.

"Legal Entity" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, "control" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity.

"You" (or "Your") shall mean an individual or Legal Entity exercising permissions granted by this License.

"Source" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files.

"Object" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types.

"Work" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below).

"Derivative Works" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof.

"Contribution" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, "submitted" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as "Not a Contribution."

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5. Submission of Contributions. Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of this License, without any additional terms or conditions. Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement you may have executed with Licensor regarding such Contributions.

6. Trademarks. This License does not grant permission to use the trade names, trademarks, service marks, or product names of the Licensor, except as required for reasonable and customary use in describing the origin of the Work and reproducing the content of the NOTICE file.

7. Disclaimer of Warranty. Unless required by applicable law or agreed to in writing, Licensor provides the Work (and each Contributor provides its Contributions) on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determining the appropriateness of using or redistributing the Work and assume any risks associated with Your exercise of permissions under this License.

8. Limitation of Liability. In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise, unless required by applicable law (such as deliberate and grossly negligent acts) or agreed to in writing, shall any Contributor be liable to You for damages, including any direct, indirect, special, incidental, or consequential damages of any character arising as a result of this License or out of the use or inability to use the Work (including but not limited to damages for loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses), even if such Contributor has been advised of the possibility of such damages.

9. Accepting Warranty or Additional Liability. While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability.

END OF TERMS AND CONDITIONS




Other


Other topics that may be of interest:




How You Can Help


At the MacCoss Lab, we believe that a strong community around an open source software project can produce world-class software.  Examples abound: Firefox, Linux and projects of the Apache Software Foundation.  We are working hard to see Skyline and its parent project, ProteoWizard, live up to the standard set by these examples.  Already our efforts have been greatly aided by others inspired by our initial work.  We encourage anyone who feels they benefit from the Skyline project to consider helping improve and sustain it in any of the following ways:

  1. Sign up as a registered user of the software to help us prove the broad appeal of our software and keep development and support funded.
  2. Post a statement explaining how your work has benefitted from using Skyline to encourage further growth in the project community.
  3. Publish or present your targeted proteomics work citing the Skyline manuscript, using Skyline graphs in your figures, and/or making your Skyline documents publicly available.
  4. Help a friend or collaborator get started using Skyline.
  5. Post to the support board your questions and comments.
  6. Take the time to work through an issue with the Skyline team and explain how the software might be improved to avoid others encountering it.
  7. Contribute a tutorial or tip.  Follow the example of existing tutorials and tips, and explain how to use features that are important to you.
  8. Contribute development time to the open source project, if you are a programmer.

Join the growing community of contributors that have helped to make Skyline what it is today.




Get Involved


Jobs
The Skyline jobs board helps employers and job seekers interested in Skyline, Panorama and targeted mass spectrometry connect.

Contribute
Make a tax-deductible contribution to the Skyline project this year through the University of Washington Foundation

Comment
See what the community is saying about Skyline - and add your statement!

Share
Other ways you can help




3rd-Party Software


Software Support: 

The following organizations have made crucial software contributions to the Skyline project.

SCIEXAgilent Technologies
Shimadzu
Thermo ScientificWaters
 
The Most Intelligent Add-In To Visual Studio
A cross-platform numerical analysis and data processing librarySubversion plug-in for Visual Studio



Related


Dashboard
Skyline adoption and use information

Panorama
Create a new project for your lab or group on PanoramaWeb hosted by the University of Washington

Or, host your own Panorama installation by joining the Panorama Partners Program

ProteoWizard
Skyline source code is available under Apache 2.0 License and part of the ProteoWizard project (mzML and mzXML conversion)

Spectral Library Links
PeptideAtlas
NIST
GPM




Funding


Current Financial Support:

Title: Seattle Quant: A Resource for the Skyline Software Ecosystem
R24 GM141156-01 (PI: MacCoss)                5/1/2021 – 4/30/2026
The grant provides support for the continued development, maintenance, instruction, and support of the entire Skyline Software Ecosystem for targeted mass spectrometry data processing, QC, assay development, and discemination.

Title: Comprehensive Biology: Exploiting the Yeast Genome
P41 GM103533 (PI: MacCoss)                      9/1/2011 – 12/31/2022
This is a biotechnology resource center.  Dr. MacCoss’ role in the center is to develop quantitative mass spectrometry based technology for the measurement of protein dynamics.  This center will support training in the use of Skyline to the proteomics community. Furthermore, it supports the development of a webservices interface to access data within the Yeast Resource Center public data repository via Skyline.

Title: Support of Agilent Mass Spectrometers within the Skyline and Panorama Software Projects
Industry Gift from Agilent (PI: MacCoss)           5/1/2012 – 12/31/2021
We are continuing to extend our analytical software tools to support Agilent mass spectrometers.

Title: Support of Bruker Mass Spectrometers within the Skyline and Panorama Software Projects
Software Engineering Contract from Bruker (PI: MacCoss)           8/1/2012 – 1/31/2023
We are continuing to extend our analytical software tools to support Bruker mass spectrometers.

Title: Support of SCIEX Mass Spectrometers within the Skyline and Panorama Software Projects
Software Engineering Contract from SCIEX (PI: MacCoss)           1/1/2015 – 12/31/2021
We are continuing to extend our analytical software tools to support SCIEX mass spectrometers.

Title: Support of Shimadzu Mass Spectrometers within the Skyline and Panorama Software Projects
Software Engineering Contract from Shimadzu (PI: MacCoss)           1/15/2014 – 1/14/2022
We are continuing to extend our analytical software tools to support Shimadzu triple quadrupole mass spectrometers.

Title: Support of Thermo Fisher Mass Spectrometers within the Skyline and Panorama Software Projects
Software Engineering Contract from Thermo Fisher (PI: MacCoss)           3/14/2014 – 3/13/2022
We are continuing to extend our analytical software tools to support Thermo Fisher mass spectrometers.

Title: Support of Waters Mass Spectrometers within the Skyline and Panorama Software Projects
Software Engineering Contract from Waters (PI: MacCoss)           9/1/2013 – 12/31/2021
We are continuing to extend our analytical software tools to support Waters mass spectrometers.

Prior Financial Support:

Title: Skyline Targeted Proteomics Environment
R01 GM103551 (PI: MacCoss)                9/14/2011 – 4/30/2021
The grant provided support for the continued development and maintenance of the widely used Skyline targeted proteomics software tool. It was superseded on 5/1/2021 by the Seattle Quant R24.

Title: The Chorus Project: A Sustainable Cloud Solution for Mass Spectrometry Data
R01 GM121696 (PI: MacCoss)                      2/1/2016 – 1/31/2021
Large-scale mass spec file storage and pipeline processing. Replaced on 5/1/2021 by the Seattle Quant R24.

Title: Library of Integrated Network-Based Cellular Signatures
U54 HG008097 (MPI: Jaffe)                7/1/2014 – 6/30/2020
This is a LINCS program grant to derive molecular signatures resultant from cellular perturbation.  We will develop a repository to disseminate multiplex mass spectrometry based assays via the Skyline client for use on all major mass spectrometry vendors.

Title: Self Correcting Nanoflow LC-MS for Clinical Proteomics
R01 GM107806 (PI: MacCoss)                                                            7/1/13 – 4/30/2017
The primary goal of this project is to improve the quality, reliability, and interlaboratory comparability of peptide mass spectrometry data. We are adding quality control capabilities to the Skyline software tool.  Furthermore, we are improving the interaction of Skyline with the instrument hardware and chromatography system.

Title: Data Acquisition and Analysis Strategies for Improving the Analysis of Peptide Mixtures Using Thermo Fisher Mass Spectrometers
Industry Sponsored Research Agreement (PI: MacCoss)           6/15/2010 – 6/15/2014
We are developing methods of analyzing mass spectrometry data on ThermoFisher mass spectrometers and Pierce reagents using Skyline.  This agreement is renewed yearly and we expect that the funding will be extended.

Title: Validating Protein Pathway Information – Integrating Proteomic Data with Transcriptomic or Metabolomic Data Sets
Industry Gift (PI: MacCoss)                                                              10/1/2011 - 9/31/2012
We are improving the interface between Agilent’s popular expression analysis software GeneSpring GX and Skyline.

Title: Genetic Regulation of Surfactant Deficiency
R01 HL082747 (PI: Cole  PI Subcontract: MacCoss)                        5/1/2011 – 3/31/2012
Goal was to understand the genetic and molecular mechanisms that disrupt pulmonary surfactant metabolism.  This project has supported the development of software and methodology for establishing targeted protein assays for Surfactant Protein-B.

Title: Label Free Differential Protein Analysis
University of Pittsburgh Contract                                                  7/1/2011 – 9/15/2011
Bridging funding to support the addition of label free MS1 quantitative analysis capabilities within Skyline.

Title: Clinical Proteomic Technology Assessment for Cancer (CPTAC)
U24 CA126479-S2 (PI: Liebler  PI Subcontract: MacCoss)               8/1/2009 – 7/31/2011
Funding provided to develop software to support the CPTAC centers for targeted proteomics method development and data analysis.




Dashboard


Learn more about the adoption and growth of Skyline use for targeted proteomics around the world.

View the Skyline 500 Report to see how the cities of the world rank for visits to the Skyline web site. The Skyline web site has seen over 45,000 users over the past 6 months, only 38.7% of which came from the United States

Skyline 500

There have been over 135,000 new installations of Skyline since it was first publicly released at ASMS 2009, with 1485 installations on average each month over the past 6 months.

Skyline Installations
* - Individuals may have installed more than once or to multiple computers in this time

 

Skyline version 21.1 released to great interest (over 17,000 instances in 7 days).

Skyline Current Use
* - Individuals may start multiple instances of Skyline in a day or use a single instance for longer than a week




Team


The following team members have made invaluable, direct contributions to the effort to build Skyline:

Brendan MacLean Brendan MacLean - principal developer
Brendan worked at Microsoft for 8 years in the 1990s where he was a lead developer and development manager for the Visual C++/Developer Studio Project. Since leaving Microsoft, Brendan has been the Vice President of Engineering for Westside Corporation, Director of Engineering for BEA Systems, Inc., Sr. Software Engineer at the Fred Hutchinson Cancer Research Center, and a founding partner of LabKey Software. In this last position he was one of the key programmers responsible for the Computational Proteomics Analysis System (CPAS), made significant contributions to the development of X!Tandem and the Trans Proteomic Pipeline, and created the LabKey Enterprise Pipeline. Since August, 2008 he has worked as a Sr. Software Engineer within the MacCoss lab and been responsible for all aspects of design, development and support in creating the Skyline Targeted Mass Spec Environment and its growing worldwide user community.

 

Nat Brace - project manager - outreach & user education
Nat worked full-time for Microsoft from 1991 through 2000 where he led a team of system engineers who were helping organizations plan for and integrate Microsoft’s advanced server solutions including network and database products, as well as software development tools. He continued at Microsoft as a consultant from 2000 to 2011, with several internal teams as a technical project owner, customer outreach lead and marketing manager. More recently, Nat joined a social innovation start-up piloting a global educational reform initiative where he served as the lead project manager in delivering a collaboration platform for use by the initiative’s participating educators, researchers and sponsors. As project manager for the Skyline team, Nat is responsible for outreach programs, like webinars, courses and user meetings, foreign language translation, and instrument vendor interactions.

Matthew Chambers Matthew Chambers - development (ProteoWizard)
Matt has worked in mass spectrometry informatics (mostly proteomics) since 2005; the first ten years he worked for David Tabb and Bing Zhang at Vanderbilt University Medical Center, and since then he has continued working as an independent consultant. He has worked in many subfields within MS, including shotgun proteomics database search, sequence tagging, spectral library search, and protein assembly. Along with Darren Kessner (director: Parag Mallick), Matt developed ProteoWizard, a free open-source library for mass spectrometry data processing. Since 2009, he has been its principal developer. The ProteoWizard tool msconvert is widely used for converting mass spectrometry data by users all over the world. For Skyline, he has focused on being able to read data directly from vendor proprietary data formats.
Rita Chupalov Rita Chupalov development
Rita’s experience with software and computers goes back to a Russian clone of DEC’s PDP-11 in 1991. She finished her degree in Organic Chemistry from Saint-Petersburg State University in 1996 where she wrote her first mass-spectrometry software: identification of halogen isotopic multiplets in low-resolution mass-spectra. Since then she worked for multiple software development companies specializing on database-centric applications, analytics and data warehousing. Her most recent job was with Amazon where she learned big data and cloud technologies.

Brian Connolly Brian Connolly - IT
Over the years Brian has worked for a number of companies in the Seattle area including Microsoft, BEA Systems and Cray. In 2007 Brian joined LabKey where he wore a number of hats. He helped LabKey's customers design and operate their LabKey Servers and pipelines. He architected and operated all of LabKey's Servers running in the public cloud (AWS and other cloud vendors) and became an expert in FISMA and HIPAA regulations. As part of the Skyline Team, Brian is responsible for managing growth of the PanoramaWeb.org and Skyline.ms servers and helping the team grow its use of the AWS cloud.
Ali Marsh Ali Marsh - development intern
Ali is the newest intern on the team. She is three years into her Bachelors degree in Computer Science at MIT. From her previous work at MIT's Energy Initiative and Seattle-based Olis Robotics, she's found an appreciation for creating intuitive user interfaces as well as aesthetic design. Ali is excited to be working on tools that will benefit the scientific community.
Brian Pratt Brian Pratt - development, support
Brian's love affair with computing started the day he and his dad unboxed that brand new Apple II. Since then he's been involved with software development for, and started a couple of companies around, such varied applications as robot-assisted surgery, circuit board manufacturing and test, internet firewalls, and proteomics. Brian's proteomics work prior to joining the Skyline team included contributions to TPP, X!Tandem, LabKey's CPAS, and ProteoWizard. He's excited to be on a team of software professionals that value performance, reliability, and usability in the support of science.
Henry Sanford Henry Sanford - development intern
Henry is studying biomedical and health informatics at the University of Washington. His first task as a development intern was to improve a menu for importing transition lists. He is excited to contribute to an open-source tool used for research.

Vagisha Sharma Vagisha Sharma - development, support, documentation (Panorama)
Vagisha got involved with proteomics at UC San Diego where she worked with Prof. Vineet Bafna. During that time she built her first tools for visualizing Mass Spectrometry data while working at ActivX Biosciences. Since moving to Seattle Vagisha has worked on Mass Spectrometry pipelines for the Aebersold group at the Institute for Systems Biology, and developed a data management system while at the University of Washington Proteomics Resource and the Yeast Resource Center. She joined the Skyline team in October, 2011. Vagisha enjoys developing tools that help researchers get stuff done.

Nicholas Shulman Nicholas Shulman - development, support
Nick worked from 1995-2000 at Microsoft on the Microsoft Access team, leaving to join Westside Corporation with Brendan to create browser-based database design tools. After Westside was acquired by BEA Systems, Nick created a new graphical JSP designer for Weblogic Workshop, an award winning Integrated Development Environment for enterprise Java applications. At LabKey Corporation, Nick created the flow cytometry module and the graphical query designer. Since March, 2009 he has worked in the Maccoss lab on Skyline and Topograph, a quantitative analysis tool for protein turnover experiments.
Kaipo Tamura Kaipo Tamura - development, support
Kaipo completed a CS degree at Washington State University in 2012, where he was introduced to proteomics as part of a senior project. He developed lipid identification software at the Pacific Northwest National Laboratory in 2012 before joining the Department of Genome Sciences at the University of Washington. Kaipo helps develop Crux in the Noble Lab, and BiblioSpec in the MacCoss Lab. He also implemented the Skyline Tool Store and is responsible for the Import Peptide Search wizard.

 

Previous contributors:

  • Susan E. Abbatiello, Ph.D. - software design, data acquisition, scientific consulting (Broad Institute, now Northeastern University)
  • Dario Amodei - development - Stanford (Baidu, Google, now OpenAI, SF)
  • Eva Baker - development (now UW Med. School)
  • Jarrett Egertson - develpment - UW (MSX and overlapped demux)
  • Gregory Finney, Ph.D. - development - UW (Crawdad)
  • Barbara Frewen - development - UW (BiblioSpec, Thermo BRIMS, now Zymergen)
  • Randall Kern - development architecture consulting (Microsoft, now SalesForce.com)
  • Don Marsh - development (now Whitemarsh Forests)
  • Birgit Schilling, Ph.D. - software design, data acquisition, scientific consulting, documentation (Buck Institute)
  • Daniela Tomazela, Ph.D. - software design, data acquisition, scientific consulting (now Merck)

Previous interns:

  • Yuval Boss - development intern - UW (now NOAA)
  • Daniel Broudy - development intern - Harvard (now Google, Seattle)
  • John Chilton - development intern - UW
  • Henry Estberg - development intern - UC Santa Cruz
  • Mimi Fung - development intern - UW (now Microsoft)
  • Max Horowitz-Gelb - development intern - U. Wisconsin (now Google, Seattle)
  • Shannon Joyner - development intern - CMU (Cisco Meraki, Cornell, now Afresh)
  • Hanna Kidanemariam - development intern - Dartmouth College
  • Alana Killeen - development intern - UW (Microsoft, DropBox, now Nautilus Biotech)
  • Trevor Killeen - development intern - UW (Facebook, now Stripe)
  • Surya Mani - development intern - Hamilton College
  • Alex MacLean - development intern - Roosevelt High School (intern - Microsoft Research, now Cal Poly CS, intern 2020-21 - DropBox)
  • Rohith Mondavilli - web development intern - Dartmouth College(now intern at Apple)
  • Tobias Rohde - development intern - UW (now intern at AI2 Incubator)
  • Pradyoth Vemulapati - development intern - UW (now OpenMarket)