Wide Quadrupole RF Window Scanning With Multi-Energy Fragmentation
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Solution Overview
Problem
Conventional data-independent acquisition (DIA) workflows in tandem mass spectrometry face challenges in de-convolving co-eluting product ions due to the non-specific nature, which limits the provision of sufficient precursor ion information for deconvolution.
Innovation Solution
Fragmenting each precursor ion isolation window multiple times with varying fragmentation parameters, including low and increasingly aggressive collision energies, to produce combined product ion spectra that allow for the correlation of precursor and product ions.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional DIA workflows use a single fragmentation parameter per precursor ion window, then the acquisition speed is maintained, but the ability to de-convolve co-eluting product ions and identify precursor ions is insufficient
Solution Approach 1:
The patent segments the fragmentation process by dividing it into multiple stages with different collision energy values. Instead of using a single fragmentation parameter, the system performs sequential fragmentations at low, medium, and high collision energies, each providing complementary information about precursor ions. This segmentation allows detailed spectral analysis without sacrificing overall acquisition throughput.
Solution Approach 2:
The system implements periodic action by cycling through multiple collision energy values in a systematic sequence for each precursor ion window. This periodic variation in fragmentation parameters enables comprehensive product ion spectral acquisition across different energy levels, improving precursor identification while maintaining structured data collection rhythm.
2Quantity of substance
If wide precursor ion isolation windows are used in DIA, then the comprehensiveness of data collection is improved, but the complexity of de-convolving co-eluting product ions increases
Solution Approach 1:
The patent applies local quality by tailoring the fragmentation conditions to specific regions of the precursor ion spectrum. Different collision energy values are applied systematically across the m/z range, with each energy level providing optimized fragmentation patterns for specific mass regions. This localized optimization within the wide window enables better resolution of co-eluting ions without reducing overall coverage.
Solution Approach 2:
The system adds another dimension to the data by introducing collision energy as an additional parameter beyond just m/z and intensity. This dimensional expansion creates a multi-dimensional spectral space where co-eluting product ions can be distinguished not only by their mass-to-charge ratio but also by their fragmentation patterns at different energy levels, thereby simplifying the de-convolution process despite wide window coverage.
3Loss of information
If multiple fragmentations are performed per precursor ion window with varying collision energies, then precursor ion information is enhanced, but the time required for data collection increases
Solution Approach 1:
The system performs preliminary action by first acquiring low collision energy spectra that provide intact precursor ion information and minimal fragmentation. This initial low-energy scan establishes a baseline for precursor identification before proceeding to higher energy fragmentations. This preliminary step optimizes information gain while minimizing redundant data collection at higher energies.
Solution Approach 2:
The patent implements dynamics by adaptively adjusting the number and energy levels of fragmentations based on the specific characteristics of each precursor ion window. Rather than applying a fixed multi-energy protocol uniformly, the system dynamically selects collision energy values and repetition counts tailored to the observed ion populations, thereby reducing unnecessary measurement time while preserving essential precursor information.
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 enhances the reproducibility and comprehensiveness of data collection by providing additional precursor ion information, enabling effective de-convolution of co-eluting product ions and improving the identification of precursor ions.
Implementation Method 1
an ion source that receives a sample and ionizes the sample, producing an ion beam
Implementation Method 2
Fragmenting each precursor ion isolation window multiple times with varying fragmentation parameters, including low and increasingly aggressive collision energies
Data Source
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AI summary
A sample is ionized using an ion source and the ion beam is received using a tandem mass spectrometer. An m/z range is divided into two or more precursor ion isolation windows. Two or more values for a fragmentation parameter are selected. A first value of the two or more values for the fragmentation parameter has a level that fragments a minimal amount of ions of the ion beam. The one or more additional values have increasingly aggressive levels that produce increasingly more fragmentation of the ions of the ion beam. For each precursor ion isolation window, the tandem mass spectrometer is instructed to perform a selection and fragmentation of the ion beam using the precursor ion isolation window and the first value and is instructed to perform one or more additional selections and fragmentations of the ion beam using the precursor ion isolation window and using the one or more additional values.