A Streamlined High-Throughput Plasma Proteomics Platform for Clinical Proteomics with Improved Proteome Coverage,...

Area of Science:

• Clinical proteomics
• Mass spectrometry
• Biomarker discovery

Background:

• Clinical proteomics demands high throughput, reproducibility, and coverage for diagnosis and personalized medicine.
• Achieving these requirements simultaneously presents a significant challenge.

Purpose of the Study:

• To develop a streamlined High-Throughput Plasma Proteomics (sHTPP) platform.
• To balance proteome coverage, throughput, and reproducibility for clinical applications.

Main Methods:

• Utilized 96-well plates, simplified sample preparation, and a disposable trap column.
• Employed a robust liquid chromatographic system with data-independent acquisition in tandem mass spectrometry.
• Integrated DIA-NN, FragPipe, and a peptide spectral library for data analysis.

Main Results:

• Achieved a throughput of 60 samples per day.
• Consistently identified over 600 protein groups, including 57 FDA-approved biomarkers, from human plasma.
• Demonstrated high quantitative completeness (>85% with 100% completeness) across 300 samples.

Conclusions:

• The sHTPP platform offers a balance between proteome coverage, throughput, and reproducibility.
• This platform shows promise for clinical settings requiring rapid and reliable large-scale sample analysis.
• Facilitates clinical medicine needs in diagnosis, prognosis, and personalized medicine.