Fragment Ion Graph Assembly for LC-MS/MS Structure Estimation

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Solution Overview

Problem

Existing methods for estimating the molecular structure of a parent molecule from fragment ions in LC-MS/MS analysis face computational challenges due to the exponential increase in computation time and the NP-complete nature of subgraph isomorphism, making it impossible to solve the combination problem within polynomial time.

Innovation Solution

A method and system that utilize a fragment ion graphing technique, including a tree search operation to assemble fragment ion graphs efficiently, using a spectrum-molecular structure database to derive candidate structures and determine the molecular structure of the target substance.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If exhaustive search of all structural combinations of fragment ions is performed to estimate parent molecule structure, then estimation accuracy is improved, but computation time increases exponentially

Engineering Contradiction:

Improvestructure estimation accuracyVSAvoidcomputation time

Core Design Contradiction:

Measurement precisionVSLoss of time

Solution Approach 1:

The patent segments the exhaustive search problem into two phases: (1) generate candidate structures for each fragment ion independently using spectral databases, and (2) assemble these candidates using graph-based methods with pruning. This segmentation avoids the exponential complexity of treating all fragment combinations as a single exhaustive search problem, enabling polynomial-time solution while maintaining accuracy.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The patent performs preliminary action by pre-generating candidate structures for each fragment ion using spectral database matching before the assembly step. This preliminary structuring of candidate solutions allows the subsequent graph assembly to work with a reduced search space, transforming the exponential problem into a polynomial-time solvable problem through pre-organized candidate sets.

Inventive Principle:

Principle #10Preliminary action

2Reliability

If all subgraph combinations are explored to assemble fragment ions, then complete structure coverage is achieved, but computational complexity becomes NP-complete

Engineering Contradiction:

Improvestructure assembly completenessVSAvoidcomputational complexity

Core Design Contradiction:

ReliabilityVSDevice complexity

Solution Approach 1:

The patent extracts the computationally intensive subgraph isomorphism problem from the overall assembly process and replaces it with an efficient graph matching algorithm that operates in polynomial time. By extracting and replacing this specific NP-complete subproblem with a simplified approach that maintains essential functionality, the overall system achieves polynomial-time complexity while preserving assembly completeness.

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The patent substitutes the mechanical exhaustive search mechanism with a graph-theoretic approach using node assignment and tree search. This substitution replaces the brute-force enumeration of all subgraph combinations with a structured graph matching process that inherently avoids redundant computations, reducing complexity from NP-complete to polynomial time while maintaining reliability.

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

3Measurement precision

If multiple candidate structures are considered for each fragment ion, then structural accuracy is improved, but the number of assembly cases increases exponentially

Engineering Contradiction:

Improvefragment ion structure accuracyVSAvoidassembly efficiency

Core Design Contradiction:

Measurement precisionVSProductivity

Solution Approach 1:

The patent introduces dynamics by implementing a tree search with pruning that adaptively explores candidate assemblies. The search dynamically prunes branches that cannot lead to valid solutions based on graph matching constraints, allowing the system to efficiently handle multiple candidates per fragment ion without exponential growth in assembly cases. This dynamic pruning maintains accuracy while preserving productivity.

Inventive Principle:

Principle #15Dynamics

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

Enables the estimation of molecular structures within polynomial time by minimizing duplicate path visits and reducing computational resources, allowing for accurate determination of the parent molecule's structure.

Implementation Method 1

strong energy is applied to sample molecules to ionize and fragment the molecules

Methodology Applied

Scientific EffectIonization: Ionisation

Implementation Method 2

the mass is measured based on the speed of each fragment ion

Methodology Applied

Scientific EffectTime of flight mass measurement: Time of Flight

Data Source

PatentUS20260023059A1Method and System for Acquiring Molecular Structure of Parent Molecule From Fragment Ions from LC-MS/MS

Publication Date: 2026.01.22 LG CHEM LTD

AI summary

A method of acquiring mass spectrum peak data of fragment ions from mass spectra for fragment ions generated in an LC-MS/MS measuring instrument may include acquiring a molecular structure of the fragment ions and fragment ion graph data by using the acquired data, and deriving a candidate molecular structure of a target substance by assembling fragment ion graphs.