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Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics.

Kendra J Adams1,2, Brian Pratt3, Neelanjan Bose4

  • 1Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina 27701, United States.

Journal of Proteome Research
|January 28, 2020
PubMed
Summary

Skyline, an open-source software, now supports small molecule quantification in mass spectrometry. This vendor-independent tool enhances targeted analysis for metabolites and biomolecules across various instruments.

Keywords:
Skylinedata analysisliquid chromatographymetabolitemetabolomicsquantitativesmall moleculestandem mass spectrometrytargeted

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Area of Science:

  • Analytical Chemistry
  • Biochemistry
  • Computational Biology

Background:

  • Lack of vendor-independent software for small molecule and metabolite quantification, particularly for targeted analysis.
  • Existing tools often tied to specific mass spectrometry instrument vendors, limiting broader application.
  • Need for adaptable software to handle diverse biomolecular research workflows.

Purpose of the Study:

  • To describe the expansion of Skyline software for small molecule quantitative mass spectrometry.
  • To demonstrate Skyline's utility as a vendor-independent tool for targeted metabolomics and biomolecular analysis.
  • To provide guidance on using Skyline for method development and data analysis across multiple instrument platforms.

Main Methods:

  • Adaptation of Skyline's existing features (peak picking, chromatographic alignment, transition selection) for small molecule data.
  • Implementation of support for selected reaction monitoring (SRM) and high-resolution mass spectrometry (HRMS).
  • Benchmarking Skyline's performance against comparable vendor-specific software for quantitative accuracy.

Main Results:

  • Skyline successfully expanded from proteomics to small molecule analysis, becoming molecule-centric and vendor-agnostic.
  • Demonstrated comparable or superior performance to vendor software in quantitative accuracy and data processing.
  • Validated Skyline's utility with real-world applications in metabolomics and biomolecular research.

Conclusions:

  • Skyline offers a powerful, free, and open-source solution for vendor-independent targeted quantitative mass spectrometry of small molecules.
  • The software's adaptability supports diverse biomolecular research, facilitating cross-platform method development and data analysis.
  • Skyline empowers researchers by providing robust tools for metabolite quantification and broader biomolecular investigations.