Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data-Independent Acquisition

Area of Science:

• Proteomics
• Mass Spectrometry
• Analytical Chemistry

Background:

• High-resolution quantitative proteomics is crucial for biological research.
• Existing Orbitrap mass spectrometers are considered the gold standard but have limitations in throughput.
• Advancements in mass spectrometry technology are needed to increase peptide identification speed and depth of coverage.

Purpose of the Study:

• To evaluate the quantitative performance of the novel Asymmetric Track Lossless (Astral) analyzer.
• To compare the peptide quantification capabilities of the Orbitrap Astral mass spectrometer against existing state-of-the-art Orbitrap instruments.
• To assess the depth of plasma proteome coverage achievable with the Orbitrap Astral and a new enrichment protocol.

Main Methods:

• Data-independent acquisition (DIA) was employed for quantitative analysis.
• The Thermo Scientific Orbitrap Astral mass spectrometer was utilized.
• A novel extracellular vesicle enrichment protocol was developed and applied to plasma samples.

Main Results:

• The Orbitrap Astral mass spectrometer quantified 5 times more peptides per unit time compared to previous gold-standard Orbitrap instruments.
• High-quality quantitative measurements were achieved across a wide dynamic range.
• Over 5000 plasma proteins were quantified in a 60-minute gradient using the Orbitrap Astral and the new enrichment method.

Conclusions:

• The Orbitrap Astral mass spectrometer represents a significant advancement in quantitative proteomics, offering unprecedented throughput.
• The instrument provides high-quality quantitative data suitable for diverse proteomic applications.
• Combined with advanced enrichment techniques, the Orbitrap Astral enables deeper exploration of complex proteomes like the plasma proteome.