Binary Bit Matrix Representation for LC-MS/MS Peptide Identification
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Solution Overview
Problem
The computational expense of identifying peptides in samples analyzed using SWATH acquisition in tandem mass spectrometry increases significantly due to the large number of different product ions in each product ion spectrum, making it difficult to efficiently compare measured product ion spectra with theoretical peptides.
Innovation Solution
Representing product ion extracted ion chromatograms (XICs) from tandem mass spectrometry data independent acquisition (DIA) experiments as binary bit matrices, allowing for efficient comparison with stored information about known compounds by generating submatrices for each theoretical peptide and calculating probability scores.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If the number of product ions in each product ion spectrum increases to improve comprehensive sample analysis, then the coverage of sample components is improved, but the computational expense of comparing measured spectra with theoretical peptides increases significantly
Solution Approach 1:
The patent segments the large-scale spectral comparison problem into smaller sub-problems by dividing the set of product ions into multiple subsets. Each subset is processed separately through independent comparison operations with theoretical peptides, and the results are aggregated to form the final identification. This segmentation reduces the computational complexity from comparing all product ions simultaneously to multiple smaller comparison tasks that can be executed more efficiently.
Solution Approach 2:
The patent performs preliminary actions by pre-processing the measured product ion spectra before the main comparison operation. This includes organizing the spectral data into an optimized format, pre-calculating reference values, and preparing the data structure to facilitate faster subsequent comparisons with theoretical peptides. These preliminary steps reduce the computational burden during the actual identification phase.
2Reliability
If comprehensive comparison with all product ions is performed to improve identification accuracy, then the reliability of peptide identification is improved, but the time required for analysis increases
Solution Approach 1:
The patent divides the comprehensive comparison task into multiple segments that can be processed in parallel or sequential batches. By segmenting the product ion comparisons, the system maintains thoroughness in the analysis while enabling more efficient resource utilization and reducing the overall analysis time through improved computational flow.
Solution Approach 2:
The patent implements a staged comparison approach where not all product ions are compared with all theoretical peptides to the same depth. Instead, the system performs preliminary filtering and scoring, focusing computational resources on the most promising matches while performing lighter-weight comparisons for less likely candidates. This partial action approach maintains sufficient identification accuracy while significantly reducing total analysis time.
Data Source
AI summary
A plurality of product ion spectra measured over plurality of cycles for each precursor ion mass selection window of two or more precursor ion mass selection windows are received from a tandem mass spectrometer. A product ion extracted ion chroatograms (XIC) is calculated for each precursor ion mass selection window of the two or more precursor ion mass selection windows from the plurality of product ion spectra for each precursor ion mass selection window. Two or more product ion XICs are produced. A two-dimensional binary bit matrix is generated to represent each product ion XIC of the two or more product ion XICs. For each XIC of the two or more product ion XICs, the binary bit matrix is separately initialized with binary values calculated from each XIC and the initialized binary bit matrix is compared with stored information about known compounds to identify known compounds of each XIC.