Towards a standardized bioinformatics infrastructure for N- and O-glycomics

Area of Science:

• Biochemistry
• Bioinformatics
• Glycoscience

Background:

• Mass spectrometry (MS)-based analysis of glycans is crucial for understanding biological processes.
• Current bioinformatics tools and databases for glycan analysis have limitations in data and experimental transparency.
• Standardized data submission is needed to improve the reliability and reproducibility of glycomics research.

Purpose of the Study:

• To review progress in the bioinformatics analysis of protein-released N- and O-linked glycans (N- and O-glycomics).
• To propose an electronic infrastructure to address current deficits in data and experimental transparency in glycomics.
• To facilitate standardized submission of MS-based glycomics data into public repositories.

Main Methods:

• Review of current bioinformatics approaches for N- and O-glycomics.
• Proposal of a standardized workflow for data submission and reporting.
• Integration of existing repositories and guidelines: UniCarb-DR, GlycoPOST, and GlyTouCan.
• Implementation of the MIRAGE (Minimum Requirement for A Glycomics Experiment) reporting guidelines.

Main Results:

• The proposed e-infrastructure enables standardized submission of MS-based glycomics information.
• Unprocessed MS data can be stored in the GlycoPOST repository.
• Glycan structures can be registered using the GlyTouCan registry.
• The workflow supports the development and extension of a comprehensive glycan structure knowledgebase.

Conclusions:

• The developed e-infrastructure enhances data and experimental transparency in MS-based glycomics.
• Standardized reporting and data submission improve the accessibility and utility of glycomics data.
• This initiative supports the advancement of glycan structure knowledge and its applications.