Mass Spectrometry Peak Extraction for Sequence Estimation
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Solution Overview
Problem
Current methods for estimating amino acid sequences from mass spectrometry data are inefficient and prone to errors due to noise in synthesized spectra and incomplete use of fragmentation information, leading to reduced reliability and accuracy, especially as the number of fragmentation steps increases.
Innovation Solution
A mass spectrometry system that performs MSn analyses, extracts and categorizes peaks based on mass complementarity and commonality between MSm and MSm+1 spectra, calculates evaluation indices for peak reliability, and uses these to estimate amino acid sequences with improved accuracy by prioritizing peaks with high reliability and frequency.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If MSn analyses with n≥3 are performed and spectra are synthesized to increase product ion peaks, then the number of observable peaks increases, but the synthesized spectrum contains much noise and the analysis becomes time-consuming with poor reliability
Solution Approach 1:
The invention extracts only the necessary and useful information from MSn spectra by identifying and selecting peaks that satisfy specific selection criteria (presence in both MS2 and MS3 spectra, appropriate intensity ratios, etc.). This extraction process eliminates noise and irrelevant peaks from the synthesized spectrum, resolving the contradiction between increasing peak quantity and maintaining reliability.
Solution Approach 2:
The invention applies different selection criteria and weighting to different peaks based on their local characteristics (intensity ratios, presence in specific spectra, position relative to precursor ion). By evaluating each peak's reliability individually and selectively using only high-confidence peaks, the method maintains high reliability while still utilizing multiple fragmentation steps.
2Loss of information
If multiple MSn analyses are performed to obtain more fragmentation information, then more product ions are observed, but the analysis time increases significantly
Solution Approach 1:
The invention performs preliminary evaluation of peaks from multiple MSn spectra using established selection criteria before final sequence estimation. By pre-identifying and filtering reliable peaks in advance, the method maximizes information utilization from multiple fragmentation steps while avoiding time-consuming processing of unreliable or redundant peaks in the final analysis stage.
3Quantity of substance
If synthesized mass spectrum is used for sequence estimation, then more peaks are available for analysis, but the peaks include noise and the reliability becomes poor
Solution Approach 1:
The invention implements a feedback mechanism where peaks are evaluated against multiple criteria (intensity ratios, presence in specific spectra, relationship to precursor ion mass) and only those meeting the criteria are selected for sequence estimation. This feedback-based filtering ensures that only precisely identified reliable peaks are used, improving measurement precision while still utilizing multiple MSn spectra.
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
The system enhances the accuracy of amino acid sequence estimation by categorizing and evaluating peaks based on their reliability and frequency, increasing the number of usable peaks and improving the reliability of terminal series identification, thus providing more accurate sequence candidates.
Implementation Method 1
a mass spectrometry means for obtaining mass spectrum data by performing an MSm analysis (where m is any integer equal to or greater than 2)
Implementation Method 2
mass spectrometry to analyze the expression and the primary structure of proteins
Implementation Method 3
the precursor ion is fragmented using CID, and mass spectrometry is performed on the ions (product ions or fragment ions) that are generated by fragmentation
Data Source
AI summary
(EN) MS analysis, MS2 analysis, . . . , MSP analysis for peptide mixture are sequentially executed to obtain respective mass spectra (S1). At this time, an analysis in which precursor ion is changed or a different cleavage condition is set for the same precursor ion is performed plural times to put together peaks appearing in mass spectra that are obtained respectively. After the number of peaks is increased, a useful peak is extracted using commonality and complementarity of the peaks of MSm spectrum and MSm+1 spectrum and classification is performed for each type of peaks extracted to obtain an appearance frequency for each classification (S3, S4). An evaluation score on whether the extracted peak is a product ion and on a terminal is calculated based on reliability and appearance frequency that are obtained in advance (S8). The evaluation score is used in estimating sequence with the use of the extracted peak to decide and output, for example, the priority of sequence candidates (S8, S9).