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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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A simple, time- and cost-effective, high-throughput depletion strategy for deep plasma proteomics
Arthur Viode1,2, Patrick van Zalm1,2,3, Kinga K Smolen2,4
1Department of Pathology, Boston Children's Hospital, Boston, MA, USA.
Science Advances
|March 29, 2023
Summary
A new plasma depletion method allows for cost-effective, high-throughput protein detection, identifying over 1300 proteins per run. This robust technique processes 60 samples daily with no batch effect, costing only $2.5 per sample.
Area of Science:
- Biochemistry
- Proteomics
- Analytical Chemistry
Background:
- Plasma protein profiling is crucial for biomarker discovery.
- Existing methods can be costly and lack high-throughput capabilities.
- Efficient depletion of abundant plasma proteins is necessary for detecting low-abundance targets.
Purpose of the Study:
- To develop and validate a cost-effective, high-throughput plasma depletion method.
- To enable in-depth proteomic analysis of plasma samples.
- To reduce the cost and increase the efficiency of plasma sample processing.
Main Methods:
- A novel plasma depletion technique was implemented.
- The method was optimized for high-throughput compatibility.
- Validation involved processing over 3000 samples.
Main Results:
- The method enables detection of >1300 proteins per run.
- Achieved a throughput of 60 samples per day.
- Demonstrated no apparent batch effect across >3000 processed samples.
- The depletion step costs approximately $2.5 per sample.
Conclusions:
- This plasma depletion method is robust, cost-effective, and suitable for high-throughput proteomic studies.
- It significantly enhances the capacity for in-depth plasma profiling.
- The low cost and high throughput make it ideal for large-scale biomarker discovery initiatives.
