Senior Researcher Chiaki Okatani and Senior Researcher Daisuke Tominaga (currently Professor at Meiji Pharmaceutical University), Technical Staff Azusa Tomioka, Researcher Hiroaki Sakaue, and Research Group Leader Atsushi Kuno of the Cellular and Molecular Biotechnology Research Institute at AIST, Designated Professor Hiroyuki Kaji of the Integrated Glyco-Big Data Center, Institute for Glyco-core Research, Nagoya University (also a Visiting Scientist at AIST), and Project Associate Professor Shigeru Ko and Project Senior Assistant Professor Norio Gouda (at the time of the study) at the Keio University School of Medicine have developed GRable Version 1.0 (GRable), a software tool for automated analysis of protein glycosylation patterns.
Although two-stage (tandem) mass spectrometry (MS2) is the mainstream method for identifying glycopeptides, AIST has developed the Glyco-RIDGE method for identifying glycopeptide signals in single-stage mass spectrometry (MS1), enabling more comprehensive analysis than the MS2 method. The newly developed GRable supports mass spectrometry based on the Glyco-RIDGE method. By visualizing the detected glycopeptide clusters, the tool can be used to visually comprehend the diversity of glycopeptides in a sample. GRable can also be used for detailed structural analysis of specific glycoproteins and large-scale analysis of samples containing multiple glycoproteins (crude samples).
In particular, they demonstrated that site-specific glycoforms of isoforms with peptides differing at only one residue can also be detected separately. In addition, the certainty (confidence level) of the analysis results can be visualized. Furthermore, evaluation of GRable in comparison with commercially available MS2-based analysis software revealed that the former could deduce approximately four times more site-specific glycoforms, demonstrating that highly comprehensive analysis can be achieved by using GRable.
The software is available on the "GlyCosmos Portal," an official portal of the Japanese Society of Carbohydrate Research, and its use is free of charge. The technical details were published in Molecular & Cellular Proteomics.
Journal Information
Publication: Molecular & Cellular Proteomics
Title: GRable Version 1.0: A Software Tool for Site-Specific Glycoform Analysis With Improved MS1-Based Glycopeptide Detection With Parallel Clustering and Confidence Evaluation With MS2 Information
DOI: 10.1016/j.mcpro.2024.100833
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