Bioinformatics Platform for Glycation Protein Identification

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Solution Overview

Problem

Current bioinformatics techniques are inadequate for the qualitative and quantitative analysis of glycation proteins and advanced glycation end-products due to their complexity and diversity, which are difficult to identify and quantify using high-resolution mass spectrometry results.

Innovation Solution

A method involving high-resolution mass spectrometry to analyze polypeptides, convert mass spectra into MS/MS, group peptides into non-glycation and glycation categories, generate a regular pattern by normalizing ion intensities, and select novel glycation peptides and advanced glycation end-products showing similar patterns, using software like Proteome Discoverer and Mascot for identification and quantification.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If high-resolution mass spectrometry is used to analyze glycation proteins and advanced glycation end-products, then measurement precision is improved, but device complexity increases

Engineering Contradiction:

Improveidentification accuracy of glycation proteinsVSAvoidcomplexity of mass spectrometry system

Core Design Contradiction:

Measurement precisionVSDevice complexity

Solution Approach 1:

The patent introduces a bioinformatics platform as an intermediary between mass spectrometry analysis and glycation protein identification. This platform includes a database of glycation-specific mass shifts and algorithms that automatically match experimental data to known glycation patterns, simplifying the interpretation of complex mass spectrometry results without compromising identification accuracy.

Inventive Principle:

Principle #24Intermediary (Mediator)

Solution Approach 2:

The patent segments the complex analysis process into distinct modules: (1) mass spectrum acquisition, (2) data preprocessing and normalization, (3) matching against glycation-specific databases, and (4) quantitative analysis. This segmentation allows each module to be optimized independently and facilitates the use of standardized computational tools.

Inventive Principle:

Principle #1Segmentation

2Device complexity

If conventional bioinformatics techniques are used for glycation protein analysis, then device complexity is reduced, but measurement precision deteriorates

Engineering Contradiction:

Improvesimplicity of analysis methodVSAvoidquantification accuracy of advanced glycation end-products

Core Design Contradiction:

Device complexityVSMeasurement precision

Solution Approach 1:

The patent applies parameter changes by implementing specific data normalization procedures that account for the unique characteristics of glycation-modified peptides. The system adjusts mass-to-charge ratio parameters to compensate for glycation-induced mass shifts and modifies intensity parameters to normalize variations in ionization efficiency, thereby improving quantification accuracy with standard computational infrastructure.

Inventive Principle:

Principle #35Parameter changes

Solution Approach 2:

The patent creates a virtual reference library of glycation-modified peptide spectra that can be copied and applied to multiple samples. This reference library contains pre-calculated mass shifts and fragmentation patterns for common glycation sites, allowing rapid comparison and identification without requiring complex real-time analysis for each sample.

Inventive Principle:

Principle #26Copying

3Loss of information

If comprehensive glycation structure analysis is performed, then information completeness is improved, but difficulty of detecting and measuring increases

Engineering Contradiction:

Improvecompleteness of glycation protein identificationVSAvoidcomplexity of glycation peptide identification

Core Design Contradiction:

Loss of informationVSDifficulty of detecting and measuring

Solution Approach 1:

The patent implements a feedback mechanism where the bioinformatics platform continuously refines identification results by comparing detected peptides against the comprehensive glycation database. The system provides feedback on identification confidence levels and adjusts search parameters iteratively, allowing thorough analysis of glycation structures while managing detection complexity through automated decision-making algorithms.

Inventive Principle:

Principle #23Feedback

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

Facilitates efficient and accurate investigation of glycation proteins and advanced glycation end-products, enabling disease prediction and diagnosis by identifying disease markers in samples.

Implementation Method 1

obtaining mass spectrum data by analyzing the polypeptide, which is obtained by hydrolyzing the protein included in the sample, with high-resolution mass spectrometry

Methodology Applied

Scientific EffectMass spectrometry:

Data Source

PatentUS11215620B2Mass spectrometry based bioinformatics platform for high-throughput identification of glycation proteins and advanced glycation end-products

Publication Date: 2022.01.04 KOREA BASIC SCI INST

AI summary

The preset invention relates to a high resolution mass spectrometry based novel bioinformatics platform for the identification of glycation proteins and advanced glycation end-product. Particularly, the bioinformatics platform of the present invention facilitates an efficient and accurate investigation of quantitative changes of glycation proteins and advanced glycation end-products which are included in various types of samples but had not been informed yet, and uses a high resolution mass spectrometry, and thereby can be effectively used for the prediction or diagnosis of a disease including cancer by examining a disease marker in a sample.