MALDI Ion Trap Timing for Double-Stranded Oligonucleotide Detection
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Solution Overview
Problem
Existing mass spectrometry methods, such as MALDI-ITMS, are unable to analyze double-stranded oligonucleotides due to the instability of the double-stranded structure in the gas phase and interference from matrix and solvent, making it difficult to detect double-stranded oligonucleotides like siRNA.
Innovation Solution
A method using a MALDI ion trap mass spectrometer with specific settings, including a longer delay time for ion trapping and adjusted voltages, to analyze double-stranded oligonucleotides, allowing for their detection and identification.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Use of energy by moving object
If MALDI mass spectrometry is used to analyze double-stranded oligonucleotides, then ionization can be achieved, but the double-stranded structure separates due to matrix and solvent influence
Solution Approach 1:
The patent introduces a specialized matrix (e.g., 6-aza-2-thiothymine or 2,4,6-trihydroxyacetophenone) as an intermediary substance that mediates between the laser irradiation and the double-stranded oligonucleotide. This matrix absorbs laser energy and facilitates gentle ionization while minimizing disruptive interactions with the hydrogen bonds maintaining the double-stranded structure, thus resolving the contradiction between achieving ionization and maintaining structural stability.
2Adaptability or versatility
If conventional MALDI-ITMS settings are used, then single-stranded oligonucleotides can be detected, but double-stranded oligonucleotides cannot be analyzed
Solution Approach 1:
The patent systematically changes multiple parameters including delay time (extended to 50-100 μs), laser fluence (optimized to 0.3-0.6 mJ/cm²), and matrix type to create a new operational regime for MALDI-ITMS. These parameter changes enable the instrument to detect double-stranded oligonucleotides while preserving the existing capability to detect single-stranded oligonucleotides, thus resolving the contradiction between versatility and detection difficulty.
3Difficulty of detecting and measuring
If longer delay time is used for ion trapping, then double-stranded oligonucleotides can be detected, but detection sensitivity may be affected
Solution Approach 1:
The patent employs dynamic optimization of the delay time parameter, extending it from conventional values to 50-100 μs specifically for double-stranded oligonucleotide detection. This dynamic adjustment of the timing parameter allows sufficient time for the formation and trapping of ions from double-stranded structures without compromising detection sensitivity, as the extended delay time is compensated by optimized laser fluence and matrix conditions.
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 sensitive and accurate detection of double-stranded oligonucleotides, particularly siRNA, by optimizing the delay time and voltage settings in the MALDI ion trap mass spectrometer, improving detection sensitivity and reducing noise.
Implementation Method 1
an ion source based on matrix-assisted laser desorption/ionization
Implementation Method 2
an ion trap unit for trapping and ejecting ions generated in the ion source
Data Source
Figure 1
Figure 2(a)~2(c)
Figure 3(a)~3(e)
AI summary
A method for analyzing a double-stranded oligonucleotide included in a sample uses an ion trap mass spectrometer comprising an ion source based on matrix-assisted laser desorption/ionization, an ion trap unit for trapping and ejecting ions generated in the ion source, and a detection unit for detecting the ions ejected from the ion trap unit. The method involves introducing the sample into the ion source, irradiating the sample with a laser, trapping the ions generated in the ion source in the ion trap unit, and then ejecting and detecting the ions trapped in the ion trap unit. A delay time, which is the time from irradiating the sample with the laser in the ion source until applying a trapping voltage to trap ions in the ion trap unit, is set to be longer than a value preset for the ion trap mass spectrometer as a delay time for trapping ions with a mass-to-charge ratio comparable to that corresponding to the molecular weight of the double-stranded oligonucleotide. This allows for the analysis of the double-stranded oligonucleotide.