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glycolab Dinko Soic

Oxonium Browser

Overview

The Oxonium Browser enables untargeted exploration of sugar oxonium ions in shotgun proteomics data, with a particular focus on prokaryotic protein glycosylation involving rare sugars. It scans high-resolution MS2 spectra for diagnostic oxonium ion pairs (intact ion + water loss fragment), filters out peptide spectra via a SAGE database search, and provides an interactive dashboard for exploring and exporting results.

Current version: v1.1.0 (Beta)
Developed using: Thermo Orbitrap mass spectrometers (QE, Tribrid, Astral)
Deployment: Docker container with all dependencies included

How It Works

  1. SAGE database search removes MS2 spectra matching unmodified peptides
  2. Two-pass mass recalibration improves m/z accuracy using amino acid fragment reference peaks
  3. Oxonium ion detection scans remaining spectra for diagnostic sugar ion pairs within defined mass tolerance
  4. Interactive dashboard lets you filter, visualize, cluster, and export results
  5. Excel reports provide summary and detailed per-scan output

For the full technical pipeline documentation, see System Architecture.

Key Features

  • Curated sugar database with common, rare, and derivative monosaccharides, extensible with custom entries — see Sugar Database
  • Optional chemspace search against >3,300 chemically plausible monosaccharide compositions for untargeted discovery of rare sugars — see Sugar Database
  • Built-in negative controls using random test masses for empirical false discovery assessment — see Detection Metrics
  • Configurable detection parameters including mass error tolerance, intensity threshold, and amino acid marker filtering — see Detection Parameters
  • Interactive dashboard with filtering, visualization, co-occurrence clustering, and export — see Dashboard Guide

Getting Started

Requirements

  • Docker (version 19.03 or higher)
  • At least 4 GB RAM (more for Astral data)
  • At least 10 GB free disk space

Quick Start

  1. Download from SourceForge
  2. Place your .mzML, .fasta, and the provided sugar database .xlsx in the Input directory
  3. Build: docker build -t oxonium-browser .
  4. Run: docker run -it -p 8051:8051 -v "$(pwd)/Input:/app/Input" -v "$(pwd)/Output:/app/Output" oxonium-browser
  5. Open http://localhost:8051

For full instructions including Windows commands and parameter customization, see the README file included in the download.

Wiki Pages

Page Description
System Architecture Pipeline architecture, module descriptions, data flow
Dashboard Guide Walkthrough of each dashboard component
Detection Metrics Understanding spectral counts, intensity, and presence
Detection Parameters Configuring mass error, intensity threshold, and other settings
Sugar Database Curated database, custom sugars, test masses, and chemspace search

Citation

If you use this software in your research, please cite:

Soic D and Pabst M. NovoGlyco: mapping protein glycosylation in prokaryotes. bioRxiv. 2026.

Contact

Dinko Soic — soic@imsb.biol.ethz.ch
Martin Pabst — m.pabst@tudelft.nl

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