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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
Published on: November 15, 2017
In-depth analysis of a plasma or serum proteome using a 4D protein profiling method
Hsin-Yao Tang1, Lynn A Beer, David W Speicher
1Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA.
Methods in Molecular Biology (Clifton, N.J.)
|April 7, 2011
Summary
This study introduces a novel 4D proteomic profiling method for analyzing human plasma and serum. The technique enhances the detection of low-abundance disease biomarkers by reducing sample complexity.
Area of Science:
- Proteomics
- Biomarker Discovery
- Clinical Chemistry
Background:
- Human plasma and serum proteomic analysis is crucial for identifying disease biomarkers.
- Challenges include sample complexity and a wide dynamic range of protein concentrations.
- Detecting low-abundance proteins is key for specific disease biomarker identification.
Purpose of the Study:
- To develop and describe a 4D protein profiling method for comprehensive proteomic analysis of plasma and serum.
- To improve the detection of low-abundance proteins in biological samples.
- To facilitate the discovery of novel disease biomarkers.
Main Methods:
- A 4D protein profiling strategy combining abundant protein depletion, microscale solution isoelectrofocusing, 1D SDS-PAGE, and reversed-phase peptide separation.
- Liquid chromatography-tandem mass spectrometry (LC-MS/MS) for peptide analysis.
- Application to human plasma and serum samples.
Main Results:
- Routine identification of a large number of proteins across nine orders of magnitude.
- Successful detection of low-abundance proteins (ng/mL levels or lower) from small sample volumes (approx. 300 μL).
- Demonstration of comprehensive proteomic analysis capabilities.
Conclusions:
- The developed 4D proteomic profiling method effectively reduces sample complexity.
- This approach enables the comprehensive analysis of plasma and serum proteomes, including low-abundance proteins.
- The method holds significant potential for advancing disease biomarker discovery.
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