Two-Stage Database Search for Strain-Level Cell Identification
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Solution Overview
Problem
Current cell identification methods using mass spectrometry face challenges in distinguishing between different strains of cells within the same species, as ribosomal proteins exhibit high amino acid sequence preservation, leading to difficulties in precise identification at the strain level.
Innovation Solution
A cell identification apparatus employing a two-stage database search system, where the first database contains comprehensive mass lists for known cells and a second database holds partial mass lists with unique ion or molecular weights specific to each classification group, allowing for precise identification by filtering out common mass values and focusing on strain-specific differences.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If mass spectrometry is performed on ribosomal proteins for cell identification, then quick identification at species level is achieved, but identification at strain level becomes difficult due to high amino acid sequence preservation
Solution Approach 1:
The patent segments the mass spectrum data into two distinct databases: a first database containing comprehensive mass lists for species-level identification, and a second database containing partial mass lists with only strain-specific mass values. This segmentation allows the system to first identify the species quickly, then focus only on strain-specific markers for precise strain-level differentiation, thereby resolving the contradiction between speed and precision.
Solution Approach 2:
The patent extracts and isolates only the strain-specific mass values from the complete mass spectrum data, storing them separately in a second database. By taking out only the relevant strain-differentiating information and separating it from the common species-level data, the system can efficiently perform strain-level identification without being overwhelmed by redundant information, thus maintaining both speed and precision.
2Measurement precision
If comprehensive mass lists for all known cells are stored in a single database, then complete identification capability is achieved, but search time increases
Solution Approach 1:
The patent divides a single comprehensive database into two specialized databases: a first database for species-level identification containing all mass values, and a second database for strain-level identification containing only strain-specific mass values. This segmentation enables the system to perform quick species identification first, then conduct a focused strain-specific search, dramatically reducing total search time while maintaining complete identification accuracy.
Solution Approach 2:
The patent performs preliminary species-level identification using the first database before conducting strain-level identification. By first determining the species classification group and then searching only within that group's strain-specific data in the second database, the system performs a preliminary filtering action that eliminates the need to search through all possible strains across all species, thus reducing search time while preserving identification accuracy.
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 precise and quick cell identification at the strain level by increasing the difference in comparison results between test cells and genetically related cells, overcoming the limitations of conventional methods that struggle with strain-level differentiation.
Implementation Method 1
analyzing a solution containing proteins extracted from a test cell or a suspension liquid containing the test cell with a mass spectrometer using MALDI-MS (matrix assisted laser desorption/ionization-mass spectrometry) or any other mild ionizing method
Data Source
AI summary
An apparatus that identifies the type of a test cell based on a result obtained by performing mass spectrometry on the test cell includes a higher-level database, which contains mass lists that each list ion mass values of constituent components of a known cell, and a lower-level database, which contains partial mass lists that each list only strain-specific ion mass values out of the ion mass values. The higher-level database is first searched for a test mass list which is created from the result of the mass spectrometry performed on the test cell, and based on a result of the search, an organism species to be searched in the following search operation is determined. Mass values common to the organism species are subsequently deleted from the mass list for the test cell, and the mass list having undergone the deletion operation is used to search the lower-level database.