Scanning SWATH Encoding for Precursor Inference With Smaller Files
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Solution Overview
Problem
Scanning SWATH mass spectrometry requires significantly larger file storage than conventional SWATH due to overlapping precursor ion transmission windows, leading to increased processing time and computational demands for post-processing.
Innovation Solution
Real-time encoding of the scanning quadrupole dimension using a quadrupole response or precursor ion inference probability function to store summed counts and positions, reducing file size without losing information needed for precursor ion inference.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If scanning SWATH with overlapping precursor ion transmission windows is used, then precursor ion identification accuracy is improved, but file storage size increases significantly
Solution Approach 1:
The patent extracts and stores only the essential information needed for precursor ion identification - specifically the summed counts and position data from the scanning quadrupole dimension - while discarding redundant raw data. This selective extraction maintains identification accuracy while dramatically reducing storage requirements from n times larger to a manageable size.
Solution Approach 2:
The patent performs real-time encoding and summation of counts during data acquisition before storage. By pre-processing the data to calculate summed counts and positions while the experiment is running, the system eliminates the need to store and later process massive amounts of raw data, resolving the contradiction between maintaining accuracy and reducing storage size.
2Loss of information
If scanning SWATH data is stored in full detail, then complete information is preserved, but post-processing time and computational power requirements increase
Solution Approach 1:
The patent extracts only the critical information elements (summed counts and positions) needed for precursor ion inference, eliminating redundant data that would otherwise require extensive processing. This extraction maintains information completeness for the intended purpose while dramatically reducing post-processing computational burden.
Solution Approach 2:
The patent performs the computationally intensive summation and encoding operations during data acquisition rather than during post-processing. This preliminary action shifts the computational burden to the acquisition phase, allowing faster and less resource-intensive post-processing while preserving all necessary information.
3Quantity of substance
If real-time encoding with summation is applied, then file storage size is reduced, but data processing complexity during acquisition increases
Solution Approach 1:
The patent changes the data representation parameters during acquisition by summing counts across overlapping windows and encoding positions. This parameter transformation simplifies the data structure for storage while maintaining the ability to perform precursor ion inference, effectively reducing storage requirements without requiring complex post-processing algorithms.
Data Source
AI summary
A precursor ion transmission window is moved in overlapping steps across a precursor ion mass range. The precursor ions transmitted at each overlapping step by the mass filter are fragmented or transmitted. Intensities or counts are detected for each of the one or more resulting product ions or precursor ions for each overlapping window that form mass spectrum data for each overlapping window. Each unique product ion detected is encoded in real-time during data acquisition. This encoding includes sums of counts or intensities of each unique ion detected the overlapping windows and positions of the windows associated with each sum. The encoding for each unique ion is stored in a memory device rather than the mass spectral data. A deblurring algorithm or numerical method is used to determine a precursor ion of each unique ion from the encoded data.