Bioinformatics Platform for Glycopeptide Identification and Quantification

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Solution Overview

Problem

Current bioinformatics techniques for identifying and quantifying N-linked glycopeptides are inefficient and inaccurate, particularly for low-abundance glycopeptides, and often fail to provide site-specific glycosylation information, limiting their application in tumor identification and glycoprotein analysis.

Innovation Solution

A novel bioinformatics platform that utilizes high-resolution mass spectrometry to analyze glycoproteins, calculates M-scores, S-scores, E-scores, and Y-scores to identify and quantify glycopeptides, and performs correlation analysis for accurate glycopeptide identification and quantification.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If chemical cleavage is used to analyze released glycan, then glycan identification is possible, but site-specific glycosylation information is lost

Engineering Contradiction:

Improveglycan identification accuracyVSAvoidsite-specific glycosylation information

Core Design Contradiction:

Measurement precisionVSLoss of information

Solution Approach 1:

The invention extracts and retains the glycopeptide portion containing the glycosylation site information while analyzing the released glycan. By using targeted enrichment methods to isolate glycopeptides from complex mixtures, the site-specific information is preserved during mass spectrometry analysis, resolving the contradiction between glycan identification and site information retention

Inventive Principle:

Principle #2Taking out (Extraction)

2Productivity

If conventional mass spectrometry is used for glycopeptide analysis, then analysis capability is provided, but identification accuracy for low-abundance glycopeptides is insufficient

Engineering Contradiction:

Improveanalysis capabilityVSAvoididentification accuracy

Core Design Contradiction:

ProductivityVSMeasurement precision

Solution Approach 1:

The invention performs preliminary enrichment of glycopeptides from complex biological samples before mass spectrometry analysis. By using lectin-based affinity capture or immunoenrichment methods to concentrate low-abundance glycopeptides prior to analysis, the identification accuracy is significantly improved while maintaining high-throughput analysis capability

Inventive Principle:

Principle #10Preliminary action

Solution Approach 2:

The invention introduces an intermediary enrichment step using lectins or antibodies as mediators between the complex sample matrix and the mass spectrometer. This intermediary process selectively captures and concentrates target glycopeptides, enhancing their detectability and identification accuracy without compromising overall analysis productivity

Inventive Principle:

Principle #24Intermediary (Mediator)

3Ease of operation

If existing glycopeptide identification software is used, then basic identification is possible, but quantitative analysis accuracy and support for high resolution mass spectrometers are insufficient

Engineering Contradiction:

Improveidentification capabilityVSAvoidquantitative analysis accuracy

Core Design Contradiction:

Ease of operationVSMeasurement precision

Solution Approach 1:

The invention implements parameter changes in the bioinformatics pipeline by incorporating high-resolution mass accuracy constraints and advanced isotopic pattern matching algorithms. The system dynamically adjusts search parameters based on the specific mass spectrometer type and resolution, enabling accurate quantitative analysis while maintaining ease of operation through automated parameter optimization

Inventive Principle:

Principle #35Parameter changes

Applied Scientific Principles

This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.

Function Achieved in This Case

This method enables efficient and accurate identification and quantification of glycopeptides, facilitating cancer diagnosis and glycoprotein analysis, and improving the analysis of glyco-structure in biosimilar therapeutics.

Implementation Method 1

obtaining mass spectrum by analyzing polypeptides prepared by hydrolyzing glycoproteins with protease by using high resolution mass spectrometer

Methodology Applied

Scientific EffectMass spectrometry:

Implementation Method 2

peptides and glycopeptides were obtained by hydrolyzing the said standard glycoprotein sample with trypsin

Methodology Applied

Scientific EffectHydrolysis: Hydrolysis

Data Source

PatentUS9436797B2Bioinformatics platform for high-throughput identification and quantification of N—glycopeptide

Publication Date: 2016.09.06 KOREA BASIC SCI INST

AI summary

The present invention relates to a more efficient and accurate method for the identification and quantification of comparatively low abundant glycopeptides, compared with general peptides, using mass spectrum obtained by using high resolution mass spectrometer. Therefore, the method of the present invention can be effectively used for the techniques for identification of biotherapeutics and diagnosis of cancer or disease by screening glycopeptide, the disease marker (Biomarker), from various samples.