A uniform data processing pipeline enables harmonized nanoparticle protein corona analysis across proteomics core
Hassan Gharibi1, Ali Akbar Ashkarran2, Maryam Jafari3
1Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
Nature Communications
|January 6, 2024
Summary
Standardizing protein corona analysis using a unified database search significantly improves data consistency and reproducibility across multiple proteomics facilities. This harmonization is essential for reliable nanomedicine safety and efficacy assessments.
Area of Science:
- Nanotechnology
- Proteomics
- Biomolecular analysis
Background:
- Protein corona formation on nanoparticles in biological fluids is critical for nanomedicine.
- Current liquid chromatography-mass spectrometry (LC-MS/MS) analysis shows high variability across different proteomics facilities.
- Only 1.8% of proteins were consistently identified across 17 facilities in a previous study.
Purpose of the Study:
- To develop and implement a standardized, unified database search strategy for protein corona analysis.
- To improve data harmonization, reproducibility, and consistency in identifying proteins in nanoparticle corona.
- To assess the impact of sample processing steps like reduction and alkylation.
Main Methods:
- Implementation of an aggregated database search with unified parameters (variable modifications, enzyme specificity, missed cleavages).
- Application of a stringent 1% false discovery rate at both protein and peptide levels.
- Analysis of identical protein corona samples across multiple proteomics facilities.
Main Results:
- The unified search strategy dramatically harmonized proteomics data, increasing reproducibility.
- Consistency-identified unique proteins increased significantly: 35.3% shared among top 5 facilities, 16.2% among top 11.
- Omitting reduction and alkylation steps reduced total quantified peptides by approximately 20%.
Conclusions:
- Standardized procedures are crucial for reliable protein corona analysis.
- Harmonized proteomics data is vital for advancing the clinical applications of nanoscale biotechnologies.
- Optimized sample processing, including reduction and alkylation, enhances protein identification.
