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Published on: January 20, 2022
Faster, quantitative, and accurate precursor acquisition independent from ion count
Alexandre Panchaud1, Sunhee Jung, Scott A Shaffer
1Department of Medicinal Chemistry, University of Washington, Seattle, Washington, United States.
This study introduces a faster, quantitative method called precursor acquisition independent from ion count (PAcIFIC) for shotgun proteomics. PAcIFIC improves detectable dynamic range, enabling monitoring of low-abundance proteins without sample prefractionation.
Area of Science:
- Proteomics
- Analytical Chemistry
- Biochemistry
Background:
- Shotgun proteomics commonly uses data-dependent precursor ion selection.
- This method has limitations in detectable dynamic range for complex samples.
Purpose of the Study:
- To report a faster, accurate, multiplexed, and quantitative precursor acquisition independent from ion count (PAcIFIC) method.
- To demonstrate the improved performance of PAcIFIC over traditional methods.
Main Methods:
- Development and application of a data-independent acquisition strategy termed PAcIFIC.
- Utilized modern ion trap instruments for faster analysis.
- Applied high mass accuracy and isobaric tagging for quantification.
- Tested on protein standards, bacterial cell lysate, and yeast samples.
Main Results:
- Analysis time decreased by 33% to 66% with PAcIFIC.
- High mass accuracy was successfully applied to the PAcIFIC strategy.
- Demonstrated quantification capabilities using isobaric tagging.
- Monitored proteins present at less than 50 copies per cell in yeast without prefractionation.
Conclusions:
- The enhanced PAcIFIC method offers a faster and more quantitative approach to shotgun proteomics.
- PAcIFIC significantly expands the detectable dynamic range, allowing for the analysis of low-abundance proteins.
- This method is suitable for comprehensive proteomic profiling of complex biological samples.
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