GRable Version 1.0: A Software Tool for Site-Specific Glycoform Analysis With Improved MS1-Based Glycopeptide...

Area of Science:

• Glycomics
• Proteomics
• Computational Biology

Background:

• High-throughput intact glycopeptide analysis is essential for understanding glycoprotein function in health and disease.
• Current mass spectrometry-based glycoproteomics face challenges due to glycan diversity and heterogeneity.
• Site-specific glycoform analysis is critical for detailed insights into glycosylation.

Purpose of the Study:

• To develop a novel, user-friendly software (GRable) for semi-automated, comprehensive site-specific glycoform analysis.
• To improve the accuracy and depth of glycopeptide detection and interpretation using MS1-based methods.
• To facilitate the analysis of intact sialylated glycoproteins on a large scale.

Main Methods:

• Development of GRable, a browser-based software implementing the Glyco-RIDGE method.
• Incorporation of advanced algorithms including "parallel clustering" for enhanced glycopeptide detection.
• Integration of MS2 information for confidence scoring and improved accuracy in peptide-glycan assignments.

Main Results:

• GRable significantly improves the comprehensiveness of glycopeptide detection, enabling focus on specific glycan structures like pauci-mannose.
• The software accurately identifies core peptides and glycan compositions, reducing misassignments through confidence level evaluation.
• Demonstrated large-scale, in-depth site-specific glycoform analysis of intact sialylated glycoproteins using purified and crude samples.

Conclusions:

• GRable offers a powerful tool for semi-automated, site-specific glycoform analysis, complementing existing glycoproteomic approaches.
• The software enhances the understanding of protein glycosylation status and changes, providing valuable biological and clinical insights.
• GRable is freely accessible online, promoting broader application in glycomics research.