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Scanning Quadrupole Data-Independent Acquisition, Part A: Qualitative and Quantitative Characterization
M Arthur Moseley1, Christopher J Hughes2, Praveen R Juvvadi3
1Proteomics and Metabolomics Shared Resource Center for Genomic and Computational Biology, Duke University Medical Center , Durham, North Carolina 27710, United States.
Journal of Proteome Research
|September 14, 2017
Summary
A new scanning quadrupole data-independent acquisition (DIA) method offers robust label-free proteomic analysis. This advanced technique demonstrates high concordance with existing methods for complex biological samples.
Area of Science:
- Proteomics
- Mass Spectrometry
- Analytical Chemistry
Background:
- Data-independent acquisition (DIA) is crucial for comprehensive proteomic analysis.
- Existing DIA methods have limitations in analyzing complex biological samples.
- Label-free quantification offers an alternative to isotopic labeling in proteomics.
Purpose of the Study:
- To introduce and characterize a novel scanning quadrupole DIA method.
- To evaluate its performance for qualitative and quantitative label-free proteomic analysis.
- To compare its technological merits against existing DIA approaches.
Main Methods:
- Development of a novel DIA method using a scanning quadrupole, collision cell, and orthogonal acceleration time-of-flight mass analyzer.
- Optimization of analytical instrument characteristics (quadrupole transmission width, scan/integration time, chromatography) for varying sample complexities.
- Application to model proteomes including human plasma, cell lines, and bacteria.
- Qualitative and semiquantitative analysis using untargeted and targeted search strategies.
- Comparison with data acquired using data-dependent acquisition (DDA) technology.
Main Results:
- The scanning quadrupole DIA method was successfully characterized for complex biological samples.
- Optimization of parameters improved performance across different sample complexities and dynamic ranges.
- Qualitative analysis of protein digest mixtures and human cell lines showed high performance.
- Comparison with DDA data revealed over 90% concordance in detected proteins.
Conclusions:
- The novel scanning quadrupole DIA method is effective for label-free proteomic analysis of complex samples.
- The method shows technological advantages over existing DIA approaches.
- It provides high-quality qualitative and semiquantitative proteomic data with excellent concordance.
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