Reproducible Determination of High-Density Lipoprotein Proteotypes

Area of Science:

• Cardiovascular Proteomics
• Mass Spectrometry
• Biomarker Discovery

Background:

• High-density lipoprotein (HDL) is a complex particle with diverse proteins, lipids, and RNAs.
• Advancements in mass spectrometry enable proteotype analysis for large patient cohorts.
• Spectral libraries are crucial for data-independent acquisition (DIA) strategies in HDL analysis.

Purpose of the Study:

• To establish HDL proteome spectral libraries from over 300 patients.
• To benchmark DIA strategy performance for detecting HDL proteotype differences.
• To investigate HDL proteotype variations in patients with type 2 diabetes and/or coronary heart disease.

Main Methods:

• Isolation of HDL from patient plasma.
• Creation of HDL proteome spectral libraries (296 protein groups, 786 peptidoforms).
• Application of DIA mass spectrometry for proteotype determination and benchmarking.

Main Results:

• DIA approach enabled robust HDL proteotype determination.
• Identification of post-translational modifications (e.g., in APOA1) affecting HDL functionality.
• Protein and peptide quantities were more discriminative than peptidoforms for HDL proteotypes.

Conclusions:

• DIA-based HDL proteotyping provides robust digitization of HDL proteotypes.
• This method supports the analysis of larger clinical cohorts for biomarker discovery.
• The findings advance the understanding of HDL heterogeneity in disease states.