Deep Plasma Proteome Profiling by Modulating Single Nanoparticle Protein Corona with Small Molecules.

Area of Science:

• Biomolecular analysis
• Nanotechnology
• Proteomics

Background:

• The protein corona on nanoparticles (NPs) is key for plasma proteome profiling using liquid chromatography-mass spectrometry (LC-MS/MS).
• Current methods have limitations in detecting the full spectrum of plasma proteins.

Purpose of the Study:

• To investigate if small molecules can alter protein corona formation and enhance plasma proteome coverage.
• To establish a new standard for plasma proteome profiling using NPs and small molecules.

Main Methods:

• Exposing polystyrene NPs to plasma spiked with various small molecules (metabolites, lipids, vitamins).
• Analyzing protein coronas using LC-MS/MS and data-independent acquisition (DIA) proteomics.
• Employing molecular dynamics simulations to study NP-protein interactions.

Main Results:

• Spiking small molecules increased protein detection by up to 8.25-fold compared to plasma alone.
• Phosphatidylcholine alone enabled detection of 897 proteins and reduced the dynamic range by depleting abundant proteins.
• Optimized DIA with phosphatidylcholine detected 1436 proteins, and top-down proteomics identified 337 additional proteoforms.

Conclusions:

• Small molecule addition to plasma is a powerful strategy to enhance NP-based proteome profiling.
• This method significantly increases the depth and breadth of detectable plasma proteins and proteoforms.
• The approach offers a streamlined, single-NP, single-molecule method for biomarker discovery and clinical translation.