Scanning SWATH Encoding for Precursor Inference and Smaller Files

Solution Overview

Problem

Scanning SWATH mass spectrometry requires significantly more file storage than conventional methods due to overlapping precursor ion transmission windows, leading to increased processing time and power requirements for post-processing large datasets.

Innovation Solution

Real-time encoding of the scanning quadrupole dimension based on a quadrupole response function or precursor ion inference probability function, which reduces file size by storing summed counts and positions of unique product ions instead of raw detection data, allowing for efficient inference of precursor ions.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Loss of information

If scanning SWATH data is stored with full raw detection data for each overlapping precursor ion transmission window, then complete information is preserved for post-processing, but file storage size increases significantly (approximately n times larger than conventional SWATH)

Engineering Contradiction:

Improveinformation completenessVSAvoidfile storage size

Core Design Contradiction:

Loss of informationVSQuantity of substance

Solution Approach 1:

The patent extracts and stores only the essential information needed for precursor ion inference - specifically the summed counts and positions of unique product ions - rather than storing all raw detection data. This extraction approach removes redundant information while preserving the critical data needed for post-processing analysis.

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The patent performs preliminary encoding of the scanning quadrupole dimension during data acquisition, applying the quadrupole response function or precursor ion inference probability function in real-time. This preliminary processing transforms the raw data into a compressed format that preserves essential information while reducing storage requirements before the data is even stored.

Inventive Principle:

Principle #10Preliminary action

2Measurement precision

If scanning SWATH data is stored with full raw detection data, then accurate precursor ion inference can be performed, but processing time and processing power requirements increase significantly

Engineering Contradiction:

Improveprecursor ion inference accuracyVSAvoidprocessing time

Core Design Contradiction:

Measurement precisionVSLoss of time

Solution Approach 1:

The patent performs preliminary encoding of the scanning quadrupole dimension during data acquisition, applying the quadrupole response function or precursor ion inference probability function in real-time. This preliminary processing transforms the raw data into a compressed format that preserves essential information while reducing storage requirements before the data is even stored.

Inventive Principle:

Principle #10Preliminary action

Solution Approach 2:

The patent changes the parameter representation of the data by applying mathematical transformations (quadrupole response function or precursor ion inference probability function) to encode the scanning quadrupole dimension. This parameter transformation reduces the data dimensionality while maintaining the information necessary for accurate precursor ion inference.

Inventive Principle:

Principle #35Parameter changes

3Reliability

If scanning SWATH data is stored with full raw detection data, then all product ion information is preserved, but the complexity of data handling and storage infrastructure increases

Engineering Contradiction:

Improvedata integrityVSAvoidstorage infrastructure complexity

Core Design Contradiction:

ReliabilityVSDevice complexity

Solution Approach 1:

The patent extracts and stores only the essential information needed for precursor ion inference - specifically the summed counts and positions of unique product ions - rather than storing all raw detection data. This extraction approach removes redundant information while preserving the critical data needed for post-processing analysis.

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The patent changes the parameter representation of the data by applying mathematical transformations (quadrupole response function or precursor ion inference probability function) to encode the scanning quadrupole dimension. This parameter transformation reduces the data dimensionality while maintaining the information necessary for accurate precursor ion inference.

Inventive Principle:

Principle #35Parameter changes

Data Source

PatentUS12080533B2Method for real time encoding of scanning SWATH data and probabilistic framework for precursor inference

Publication Date: 2024.09.03 DH TECH DEVMENT PTE

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.