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Updated: Feb 27, 2026

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
Published on: August 19, 2025
The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics.
Lindsay K Pino1, Brian C Searle1, James G Bollinger1
1Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington.
Skyline is an open-source software that accelerates targeted proteomics experiments. It supports method development, data processing, and quantitative analysis for the mass spectrometry community.
Area of Science:
- Proteomics and Mass Spectrometry
- Bioinformatics and Computational Biology
Background:
- Targeted proteomics experiments require specialized software for efficient data acquisition and analysis.
- The proteomics community needs accessible, open-source tools to advance research.
Purpose of the Study:
- To review the informatics capabilities of the Skyline software ecosystem.
- To highlight Skyline's role in accelerating targeted proteomics experimentation.
Main Methods:
- Review of Skyline's features for method development in targeted mass spectrometry.
- Analysis of Skyline's functionalities for raw data processing.
- Examination of Skyline's tools for quantitative proteomics analysis and results sharing.
Main Results:
- Skyline provides a comprehensive informatics solution for targeted proteomics.
- The software facilitates computationally assisted method development.
- It enables efficient processing of raw data and quantitative analysis.
Conclusions:
- Skyline is a valuable, freely available resource for the proteomics and mass spectrometry community.
- Its open-source nature fosters user contribution and software improvement.
- The ecosystem supports the entire workflow from experiment design to results dissemination.
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