DDA Mass Spectrometry Using CCS-Guided Precursor Selection
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Existing mass spectrometry methods struggle to efficiently identify and analyze sub-stoichiometrically abundant modified proteins and cross-linked peptides due to their low relative abundance, leading to difficulties in selective targeting and analysis.
Innovation Solution
A method of mass spectrometry that determines collision cross section (CCS) values directly from MS1 data to selectively target precursor ions of interest in MS2 scans, prioritizing modified and cross-linked peptides by analyzing CCS-indicative values without the need for additional sample handling or enrichment.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If conventional DDA methods are used to select precursor ions for MS2 scans, then the majority of precursors selected are unmodified peptides, but modified peptides and cross-linked peptides remain under-analysed due to their sub-stoichiometric abundance
Solution Approach 1:
The invention changes the selection parameter from intensity-based (conventional DDA) to CCS-based selection. By using collision cross section values derived from MS1 data, the method identifies and prioritizes modified peptides and cross-linked peptides for MS2 scans, resolving the contradiction between low abundance and analysis efficiency
Solution Approach 2:
The invention replaces the mechanical/enzymatic enrichment steps with a computational approach using CCS values from MS1 data. This substitution eliminates the need for physical sample manipulation while achieving the same goal of enriching modified peptide analysis
2Productivity
If enrichment techniques are used to increase the abundance of modified peptides, then modified peptides can be analysed more efficiently, but additional sample handling steps are required which increase device complexity and time
Solution Approach 1:
The invention extracts the enrichment function from the physical sample handling domain and transfers it to the data analysis domain. By calculating CCS values from MS1 data and using these to select precursors, the method achieves enrichment of modified peptide analysis without removing or manipulating the physical sample
Solution Approach 2:
The MS1 data itself provides the information (CCS values) needed to select modified peptides for MS2 scans. The system uses its own measurement data to guide subsequent analysis, eliminating the need for external enrichment devices or procedures
3Productivity
If enrichment techniques are used to increase the abundance of cross-linked peptides, then cross-linked peptides can be analysed more efficiently, but additional sample handling steps are required which increase analysis time
Solution Approach 1:
The invention performs preliminary calculation of CCS values from MS1 data before MS2 scan selection. This advance preparation allows immediate identification of cross-linked peptides for MS2 analysis without intermediate enrichment steps, reducing overall analysis time
Solution Approach 2:
The invention maintains continuous data acquisition and analysis without interrupting the workflow for sample enrichment. The CCS-based selection enables seamless transition from MS1 to MS2 scans, keeping the mass spectrometer operating continuously at full capacity
Data Source
AI summary
Data Dependent Acquisition (DDA) mass spectrometry methods comprise ionising a sample to produce sample ions, analysing the sample ions with one or more MS1 mass analysis scan(s) to obtain MS1 data, identifying one or more precursor ions from the MS1 data, and then analysing the sample ions with one or more MS2 mass analysis scan(s). Each MS2 scan is targeted to one of the one or more precursor ions identified from the MS1 data. For each of one or more precursor ions identified from the MS1 data, a value indicative of a collision cross section (CCS) of that precursor ion is determined from the MS1 data. Based on the CCS-indicative value(s), precursor ion(s) are selected to target by the one or more MS2 mass analysis scan(s) and/or an order in which to target precursor ions by the one or more MS2 mass analysis scan(s) is determined.