Magnetic Bead Protein Fragmentation for Faster Mass Spectrometry
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Solution Overview
Problem
Existing sample preparation methods for mass spectrometry, particularly in MS-based proteomics, face challenges in achieving efficient and uniform fragmentation of proteins and peptides, leading to complex samples that overwhelm the capabilities of MS instruments, and require lengthy digestion times and the use of proteases that introduce contaminants and variability.
Innovation Solution
A method involving the use of a moving magnetic body to fragment proteins, polypeptides, and peptides by colliding with them under the influence of a fluctuating or oscillating magnetic field, eliminating the need for enzymatic or chemical agents and providing a more uniform and reproducible fragmentation process.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If proteases are used for enzymatic protein digestion, then sequence coverage is improved, but additional protein contamination is introduced and variability increases
Solution Approach 1:
The patent extracts and removes the harmful element (protease contamination) from the system by replacing enzymatic digestion with magnetic bead-based fragmentation, thereby eliminating the source of contamination while maintaining the useful function of protein breakdown
Solution Approach 2:
The patent replaces the biochemical/enzymatic system with a physical/mechanical system using magnetic beads to fragment proteins, substituting chemical-biological processes with mechanical forces to achieve fragmentation without introducing biological contaminants
2Productivity
If higher protease concentrations are used to increase digestion efficiency, then fragmentation speed is improved, but additional protein contamination is introduced
Solution Approach 1:
The patent replaces the biochemical system with a physical mechanical system using magnetic beads that can be precisely controlled and removed, eliminating the trade-off between digestion efficiency and contamination since the mechanical fragments can be separated from the magnetic beads after fragmentation
Solution Approach 2:
The patent enables easy discarding of the magnetic beads after they have performed their fragmentation function, allowing the fragments to be recovered for analysis while the source of potential contamination (magnetic beads) is discarded, eliminating the contamination problem inherent in using higher concentrations of enzymatic proteases
3Measurement precision
If lengthy digestion times are used to achieve complete proteolysis, then sequence coverage is improved, but processing time increases
Solution Approach 1:
The patent applies mechanical vibration through oscillating magnetic fields to the magnetic beads, enhancing the fragmentation efficiency and reducing the time required to achieve complete protein breakdown, thereby maintaining sequence coverage while significantly reducing processing time
Solution Approach 2:
The patent employs periodic oscillating magnetic fields to drive the magnetic beads, creating repeated mechanical stress on the proteins that accelerates fragmentation compared to static or single-action methods, thus achieving complete proteolysis more rapidly
4Measurement precision
If intact proteins are analyzed by top-down proteomics, then complete protein characterization is achieved, but separation and ionization efficiency decrease
Solution Approach 1:
The patent segments intact proteins into smaller fragments using magnetic bead fragmentation, creating intermediate-sized peptides that are more amenable to LC separation and ESI ionization while still providing sufficient sequence information for comprehensive protein characterization, thus resolving the contradiction between complete characterization and analytical efficiency
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 approach generates a diverse range of fragments, facilitating de novo sequencing and reducing sample complexity, while ensuring consistent fragmentation patterns and improved sequence coverage without the use of proteases, thus enhancing the efficiency of MS analysis.
Implementation Method 1
A method of preparing a sample for an analytic procedure... fragmenting said molecule using at least one moving magnetic body, wherein said at least one magnetic body performs a fluctuating or oscillating motion, wherein said motion is triggered by a fluctuating or oscillating magnetic field
Implementation Method 2
wherein said magnetic body collides with said molecule, and wherein under such circumstances energy is transferred to said molecule triggering or contributing to fragmenting said molecule
Data Source
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AI summary
The present invention provides a method of preparing a sample for an analytic procedure, said sample comprising at least one protein, polypeptide or peptide molecule, and said method comprising fragmenting said molecule using at least one moving magnetic body.