Benchmark for Quantitative Global and Redox Proteomics Analysis by Combining Protein-Aggregation Capture and Data...

Area of Science:

• Biochemistry
• Proteomics
• Oxidative Stress Research

Background:

• Oxidative damage is implicated in cardiovascular and neurological diseases.
• Thiol redox reactions are crucial for sensing oxidative stress and regulating protein function.
• Current redox proteomics methods require extensive sample manipulation and are incompatible with data-independent acquisition (DIA).

Purpose of the Study:

• To introduce PACREDOX, a novel protein aggregation capture (PAC)-based strategy for redox proteomics.
• To demonstrate PACREDOX compatibility with library-free DIA.
• To evaluate PACREDOX efficiency and coverage compared to traditional methods.

Main Methods:

• Development of PACREDOX strategy combining protein aggregation capture with mass spectrometry.
• Integration with library-free DIA using in silico spectral library correction with experimental retention time data.
• Benchmarking PACREDOX against FASILOX in a myocardial infarction model.

Main Results:

• PACREDOX reduces preparation time and costs compared to FASILOX.
• The method maintains comprehensive thiol and proteome coverage.
• PACREDOX with DIA achieved enhanced peptide and protein coverage in a myocardial infarction model, providing similar biological insights.

Conclusions:

• PACREDOX is an efficient, automatable, high-throughput, and cost-effective strategy for redox proteomics.
• This methodology facilitates the study of oxidative damage in various biological contexts.
• PACREDOX enhances the capabilities of redox proteomics, particularly when combined with DIA.