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Detection and Quantitation of Label-Retaining Cells in Mouse Incisors using a 3D Reconstruction Approach after Tissue Clearing

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Identifying intact

Jiechen Shen¹, Zexuan Chen¹, Shisheng Sun¹

¹College of Life Sciences, Northwest University, Xi'an 710069, China.

Biophysics Reports

|June 8, 2023

Summary

This summary is machine-generated.

StrucGP is a novel tool for analyzing N-glycoproteins at the site-specific level. It accurately interprets glycan structures using mass spectrometry and provides detailed analysis of glycosylation changes.

Keywords:

Glycan structure Glycoproteomics Mass spectrometry Protein glycosylation StrucGP

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Area of Science:

Biochemistry
Proteomics
Glycomics

Background:

Protein glycosylation plays a crucial role in numerous biological processes.
Analyzing site-specific glycosylation changes is vital for understanding physiological and pathological conditions.
Mass spectrometry is increasingly used for intact glycopeptide analysis.

Purpose of the Study:

To introduce StrucGP, a glycan database-independent search engine for structural interpretation of N-glycoproteins.
To demonstrate a workflow for site-specific glycosylation analysis using StrucGP and GlycoVisualTool.
To provide a method for accurate glycopeptide analysis accessible to researchers with basic proteomic knowledge.

Main Methods:

Utilizing StrucGP, a glycan database-independent search engine.
Implementing dual collision energies in mass spectrometry for peptide and glycan fragment separation.
Estimating false discovery rates (FDR) for peptides and glycans, and calculating detailed structure probabilities.
Employing an in-house software, GlycoVisualTool, for result inspection and visualization.

Main Results:

StrucGP enables site-specific structural interpretation of N-glycoproteins.
The implemented dual collision energy strategy enhances accuracy in fragment analysis.
The workflow allows for robust estimation of FDR and detailed glycan structure probabilities.
GlycoVisualTool facilitates effective inspection and visualization of analysis results.

Conclusions:

StrucGP provides a powerful and accurate method for site-specific N-glycoprotein analysis.
The demonstrated workflow is user-friendly for researchers with basic proteomic expertise.
Accurate glycopeptide analysis using StrucGP aids in understanding glycosylation's role in biological systems.