If you use Skyline in your experiments, please cite our Bioinformatics Application Note, listed below.
If you use Skyline MS1 filtering, please cite our Mollecular Cellular Proteomics paper, listed below.
If you use Skyline for collision energy optimization, please cite our Analytical Chemistry paper, listed below.

Peer reviewed manuscripts:

  • MacLean, Bioinformatics 2010 article (cited by 1317)
    Skyline: An Open Source Document Editor for Creating and Analyzing Targeted Proteomics Experiments
    [abstract][pdf]
  • Pino, Mass Spectrometry Reviews 2017 article
    The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics
    [abstract]
  • Bereman, Journal of Proteome Research 2016 article (cited by 6)
    An Automated Pipeline to Monitor System Performance in Liquid Chromatography Tandem Mass Spectrometry Proteomic Experiments
    [abstract][pdf]
  • Sharma, Journal of Proteome Research 2014 article (cited by 63)
    Panorama: A Targeted Proteomics Knowledge Base
    [abstract][pdf]
  • Broudy, Killeen, Bioinformatics 2014 article (cited by 19)
    A framework for installable external tools in Skyline
    [abstract]
  • Egertson, Nature Protocols 2015 article (cited by 44)
    Multiplexed peptide analysis using data-independent acquisition and Skyline
    [abstract]
  • Abbatiello, Mollecular Cellular Proteomics 2015 article (cited by 72)
    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 article (cited by 134)
    Multiplexed MS/MS for improved data-independent acquisition
    [abstract]
  • Abbatiello, Mollecular Cellular Proteomics 2013 article (cited by 65)
    Design, Implementation, and Multi-Site Evaluation of a System Suitability Protocol for the Quantitative Assessment of Instrument Performance in LC-MRM-MS
    [abstract]
  • Glukhova, Journal of Proteome Research 2013 article(cited by 5)
    Rapid assessment of RNAi-mediated protein depletion by selected reaction monitoring (SRM) mass spectrometry
    [abstract]
  • Schilling, Mollecular Cellular Proteomics 2012 article (cited by 191)
    Platform independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in Skyline. Application to protein acetylation and phosphorylation
    [abstract]
  • Sherrod, Journal of Proteome Research 2012 article (cited by 39)
    Label-Free Quantitation of Protein Modifications by Pseudo-Selected Reaction Monitoring with Internal Reference Peptides
    [abstract]
  • Escher, Proteomics 2012 article (cited by 156)
    Using iRT, a normalized retention time for more targeted measurement of peptides
    [abstract]
  • Bereman, Proteomics 2012 article (cited by 50)
    The development of selected reaction monitoring methods for targeted proteomics via empirical refinement
    [abstract]
  • Stergachis, Nature Methods 2011 article (cited by 86)
    Rapid empirical discovery of optimal peptides for targeted proteomics
    [abstract]
  • MacLean, Analytical Chemistry 2010 article (cited by 142)
    Effect of Collision Energy Optimization on the Measurement of Peptides by Selected Reaction Monitoring (SRM) Mass Spectrometry
    [abstract]
  • Prakash, Journal of Proteome Research 2009 article (cited by 144)
    Expediting the Development of Targeted SRM Assays: Using Data from Shotgun Proteomics to Automate Method Development
    [abstract]

Presentations and posters:

  • 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]

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