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🔧 Skyline

Skyline

Targeted Proteomics Environment.

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Overview

Skyline is a widely used application for targeted proteomics, supporting Selected Reaction Monitoring (SRM), Parallel Reaction Monitoring (PRM), and Data-Independent Acquisition (DIA) experiments. It allows researchers to build targeted methods, process raw mass spectrometry data, and analyze the results to quantify proteins and peptides. It is developed and supported by the MacCoss Lab at the University of Washington.

✨ Key Features

  • Targeted method design for SRM, PRM, and DIA
  • Quantitative analysis of targeted proteomics data
  • Chromatogram visualization and peak integration
  • Support for data from all major MS vendors
  • Creation of spectral libraries
  • System suitability and QC monitoring

🎯 Key Differentiators

  • Completely free and open-source.
  • Vendor-neutral, supporting a wide range of instruments.
  • Active development and strong community support.

Unique Value: Provides a powerful, flexible, and free end-to-end environment for targeted mass spectrometry data analysis, fostering reproducible research.

🎯 Use Cases (5)

Targeted protein quantification Biomarker discovery and validation Analysis of DIA/SWATH-MS data Small molecule quantification Metabolomics

✅ Best For

  • The de facto standard for targeted proteomics data analysis in the academic community.
  • Used in thousands of peer-reviewed publications.

💡 Check With Vendor

Verify these considerations match your specific requirements:

  • Shotgun/discovery proteomics (database searching)
  • De novo sequencing
  • Genomic analysis

🏆 Alternatives

Spectronaut Vendor-specific software (e.g., Sciex OS)

Offers a vendor-neutral, community-driven, and cost-free solution with extensive features, particularly for SRM and PRM, compared to commercial or vendor-specific tools.

💻 Platforms

Desktop

✅ Offline Mode Available

🔌 Integrations

External tools for statistical analysis (MSstats, etc.) Panorama for data sharing and repository

💰 Pricing

Contact for pricing
Free Tier Available

Free tier: Fully functional and free for everyone.

Visit Skyline Website →

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