Resonant CID of Oligonucleotide Ions for Accurate MS Sequencing
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Solution Overview
Problem
Existing mass spectrometry methods face challenges in effectively fragmenting large analytes like oligonucleotides, particularly in tracing the sequence information of middle portions, as conventional collision-induced dissociation (CID) methods often result in non-unique fragment ions that are difficult to trace back to their positions within the precursor sequence.
Innovation Solution
The method involves introducing oligonucleotides into an electrospray ionization source in negative mode for deprotonation, trapping the negatively charged ions in a radiofrequency (RF) ion trap, and applying a resonant AC excitation signal to selectively fragment the ions via collisions with buffer gas molecules, using specific electrode configurations to control ion trajectories and energies.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional collision-induced dissociation (CID) is used to fragment large analytes like oligonucleotides, then fragmentation occurs, but the fragment ions are non-unique and difficult to trace back to their positions within the precursor sequence
Solution Approach 1:
The patent applies resonant AC excitation to induce secular oscillations in trapped oligonucleotide ions at specific frequencies. This mechanical vibration approach causes selective fragmentation at defined positions along the oligonucleotide chain, generating position-specific fragment ions that can be traced back to their original locations, thereby resolving the information loss problem while maintaining measurement precision
Solution Approach 2:
The patent changes the fragmentation parameters by using resonant excitation at different secular frequencies corresponding to different ion positions. By tuning the AC excitation frequency to match specific secular frequencies of ions at different positions, the method selectively fragments the oligonucleotide at predetermined locations, enabling accurate sequence determination without information loss
2Measurement precision
If resonant AC excitation is applied to selectively fragment ions, then distinct fragment ions with unique m/z ratios are generated, but the device complexity increases due to additional electrode configurations
Solution Approach 1:
The patent employs a multipole electrode structure (such as quadrupole or hexapole rods) that serves dual functions: it provides ion trapping through RF voltages and enables resonant excitation through superimposed AC voltages. This multi-functional electrode design achieves selective fragmentation without requiring separate dedicated electrodes, thereby limiting the increase in device complexity while maintaining measurement precision
Solution Approach 2:
The patent combines the trapping and excitation functions into a single electrode system by superimposing AC excitation voltages on the RF trapping voltages. This merging of functions allows resonant fragmentation to be achieved within the existing ion trap structure, avoiding the need for additional complex electrode configurations while generating distinct fragment ions with unique m/z ratios
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 distinct fragment ions with unique m/z ratios, allowing for more accurate sequencing by preventing subsequent fragmentation and enhancing the determination of partial nucleotide sequences, particularly in the middle portions of oligonucleotides.
Implementation Method 1
introducing the oligonucleotide into an electrospray ionization source operated in a negative mode to cause deprotonation of said oligonucleotide for generating a negatively charged ion of said oligonucleotide
Implementation Method 2
trapping said negatively charged oligonucleotide ion in a radiofrequency (RF) ion trap containing a buffer gas
Implementation Method 3
using a resonant AC excitation signal to resonantly excite the negatively charged oligonucleotide ion at a secular frequency thereof to cause selective fragmentation of the negatively charged oligonucleotide ion via collision with molecules of the buffer gas
Data Source
AI summary
A method of dissociation of an oligonucleotide in a mass spectrometer includes introducing the oligonucleotides into an electrospray ionization source operated in a negative mode to cause deprotonation of said oligonucleotide for generating a negatively charged ion of said oligonucleotides, trapping said negatively charged oligonucleotide ions in linear radiofrequency (RF) ion traps with T bar electrodes, filling the linear ion trap with a buffer gas, and using a resonant dipole AC excitation signal applied to the T bar electrodes to resonantly excite the negatively charged oligonucleotide ions at secular frequencies thereof to cause selective fragmentation of said negatively charged oligonucleotide ions via collision with molecules of said buffer gas.