Full Mass Range ΦSDM Orbitrap Mass Spectrometry for DIA Proteome Analysis

Area of Science:

• Proteomics
• Mass Spectrometry
• Analytical Chemistry

Background:

• Optimizing data-independent acquisition in proteomics balances spectral resolution and speed.
• Orbitrap mass spectrometry is a key technology for quantitative proteomics.

Purpose of the Study:

• To implement and evaluate a real-time full mass range phase-constrained spectrum deconvolution method (ΦSDM) for Orbitrap mass spectrometry.
• To assess the impact of ΦSDM on spectral resolution, acquisition speed, and quantitative accuracy in proteomics.

Main Methods:

• Real-time full mass range implementation of ΦSDM on Orbitrap mass spectrometry.
• Comparison of ΦSDM with enhanced Fourier transformation (EFT) signal processing.
• Application of ΦSDM to varying chromatographic gradient lengths (21, 12, and 5 min) using HeLa digest samples.

Main Results:

• ΦSDM increased mass resolving power without increasing scan time.
• ΦSDM improved peptide quantification by 16% in a 2-hour analysis.
• ΦSDM significantly enhanced protein group and peptide identification rates (>15%) in a 5-minute gradient compared to EFT.

Conclusions:

• ΦSDM is a viable alternative signal processing algorithm for Orbitrap data.
• ΦSDM improves spectral quality and quantitative accuracy in proteomics.
• ΦSDM is particularly advantageous for fast chromatographic gradients and high peptide density regions.