Spectrum Annotator Ddzby

Universal MS/MS spectrum annotation tool for glycopeptides and crosslinked peptides.

🚀 Try the Live Demo - No installation required!

User Manual - Detailed installation and usage guide for Windows, macOS, and Linux

Features

Glycopeptide Annotation

• O-glycans: Core 1-4 structures, sialylated, phosphorylated, sulfated variants
• N-glycans: High-mannose, complex, hybrid structures
• Y ion series: Complete glycan ladder (Y0, Y1, Y2, ..., Y(core), Y(intact))
• Oxonium ions: Comprehensive diagnostic ion library

Crosslinked Peptide Annotation

• MS-cleavable: DSSO, DSBSO with stub mass identification
• Non-cleavable: BS3, DSS
• ProForma notation: Full support for crosslink annotation

Quality Assessment

• False Match Rate: Spectrum shifting method (Schulte et al., Anal. Chem. 2025)
• Annotation statistics: Coverage, matched peaks, intensity

Two Ways to Use

1. Web Interface (No coding required) - Interactive browser-based annotation
2. Python API - For batch processing and pipeline integration

See the User Manual for step-by-step instructions.

Installation

From PyPI (Recommended)

pip install spectrum-annotator-ddzby

From Source

git clone https://github.com/lfu46/GlycoSpectrumAnnotator.git
cd GlycoSpectrumAnnotator
pip install -e .

With Streamlit Web App

pip install spectrum-annotator-ddzby[streamlit]

Quick Start

Python API

from spectrum_annotator_ddzby import (
    FragmentCalculator,
    SpectrumAnnotator,
    O_GLYCAN_COMPOSITIONS,
    N_GLYCAN_COMPOSITIONS,
    CROSSLINKERS,
    generate_crosslink_fragments,
)

# Glycopeptide annotation
calc = FragmentCalculator(
    peptide="PEPTIDEK",
    modifications={"5": "HexNAc"},
    precursor_charge=3,
    glycan_type="O-GlcNAc"
)
fragments = calc.calculate_all_fragments()

# Access glycan library
print(O_GLYCAN_COMPOSITIONS['Sialyl-T'].mass)  # 656.2276 Da

# Crosslinked peptide fragments
xl_fragments = generate_crosslink_fragments(
    peptide1_mass=1000.0,
    peptide2_mass=1200.0,
    crosslinker=CROSSLINKERS['DSBSO'],
    precursor_charge=4
)

Web Interface (Streamlit)

# Run the web app
streamlit run app.py

Or visit the hosted version at: glycospectrumannotator.streamlit.app

Supported Glycan Compositions

O-Glycans (12 common human structures)

Name	Composition	Mass (Da)
Tn (O-GlcNAc)	HexNAc(1)	203.08
T-antigen	HexNAc(1)Hex(1)	365.13
Sialyl-Tn	HexNAc(1)NeuAc(1)	494.17
Sialyl-T	HexNAc(1)Hex(1)NeuAc(1)	656.23
Core 2	HexNAc(2)Hex(1)	568.21
...	...	...

N-Glycans

Name	Composition	Mass (Da)
Man5	HexNAc(2)Hex(5)	1216.42
Man9	HexNAc(2)Hex(9)	1864.63
A2G2F	HexNAc(4)Hex(5)Fuc(1)	1768.64
A2G2FS2	HexNAc(4)Hex(5)Fuc(1)NeuAc(2)	2350.83

Supported Crosslinkers

Name	Type	Spacer	Stub Masses
DSSO	MS-cleavable	10.1 Å	A: 54.01, T: 85.98, S: 103.99
DSBSO	MS-cleavable	12.5 Å	A: 54.01, T: 85.98, S: 103.99
BS3	Non-cleavable	11.4 Å	-
DSS	Non-cleavable	11.4 Å	-

Ion Types and Colors

Ion Type	Color	Description
b	Blue	N-terminal HCD ions
y	Red	C-terminal HCD ions
c	Green	N-terminal ETD ions
z	Orange	C-terminal ETD ions
Y	Purple	Glycopeptide Y ions
Oxonium	Brown	Glycan diagnostic ions
XL-stub	Cyan	Crosslinker stubs

Output Statistics

• Sequence Coverage: Fraction of peptide bonds with fragment ions
• FMR (peaks): False match rate based on peak count
• FMR (intensity): False match rate based on intensity
• Peaks Annotated: Fraction of experimental peaks matched
• Intensity Annotated: Fraction of total intensity matched

References

• Schulte, D. et al. "A Universal Spectrum Annotator for Complex Peptidoforms in Mass Spectrometry-Based Proteomics." Analytical Chemistry 2025, 97, 23120-23130.
• Brademan, D.R., Riley, N.M., Kwiecien, N.W., and Coon, J.J. "Interactive Peptide Spectral Annotator: A Versatile Web-based Tool for Proteomic Applications." Molecular & Cellular Proteomics 2019, 18(8 Suppl 1), S193-S201. DOI: 10.1074/mcp.TIR118.001209
• MSFragger Human O-glycan database

Citation

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

Fu, L. (2026). Spectrum Annotator Ddzby: Universal MS/MS spectrum annotation tool.
GitHub: https://github.com/lfu46/GlycoSpectrumAnnotator

License

MIT License - see LICENSE for details.

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

Contact

• Author: Longping Fu
• Email: [email protected]
• GitHub: @lfu46