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Extracting Informative Glycan-Specific Ions From Glycopeptide MS/MS Spectra With GlyCounter.

Kathryn Kothlow1, Haley M Schramm1, Kayla A Markuson1

  • 1Department of Chemistry, University of Washington, Seattle, Washington, USA.

Molecular & Cellular Proteomics : MCP
|October 17, 2025
PubMed
Summary
This summary is machine-generated.

Glycopeptide tandem mass spectra contain valuable glycan information. GlyCounter is a new open-source tool that rapidly extracts this glycan-specific fragment data, aiding glycoproteomic analysis.

Keywords:
data evaluationglycopeptidesglycoproteomicsinformaticstandem mass spectrometry

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Area of Science:

  • Glycoproteomics
  • Mass Spectrometry
  • Computational Biology

Background:

  • Glycopeptide tandem mass spectra contain numerous glycan-specific fragments crucial for characterizing glycan modifications.
  • Current methods for analyzing these fragments often rely on manual inspection or are limited to identified glycopeptides.
  • A systemic approach to explore glycan-informative ions and their relationships is lacking.

Purpose of the Study:

  • Introduce GlyCounter, a freely available, open-source tool for rapid extraction of glycan-specific ion information from mass spectrometry data.
  • Demonstrate the utility of GlyCounter in analyzing diverse publicly available datasets.
  • Enable researchers to refine glycoproteomic workflows, including sample preparation, data acquisition, and identification methods.

Main Methods:

  • Developed GlyCounter, an open-source software tool.
  • Designed GlyCounter to extract oxonium, Y-type, and custom ion information from raw mass spectrometry data files.
  • Applied GlyCounter to evaluate glycan-specific fragments in various public glycoproteomic datasets.

Main Results:

  • GlyCounter rapidly extracts glycan-specific ion information, including oxonium and Y-type ions.
  • Analysis of public datasets demonstrates that GlyCounter can reveal glycan characteristics without requiring database searches.
  • GlyCounter's oxonium ion analysis can supplement database searches, providing additional spectral evidence for glycopeptide identification.

Conclusions:

  • GlyCounter is a user-friendly tool that can be integrated into existing glycoproteomic workflows.
  • The software facilitates straightforward evaluation of glycan content in glycoproteomic data.
  • GlyCounter aids in refining glycoproteomic analysis, from sample preparation to data interpretation.