Comparative Evaluation of MaxQuant and Proteome Discoverer MS1-Based Protein Quantification Tools.

Area of Science:

• Proteomics
• Quantitative Mass Spectrometry
• Bioinformatics

Background:

• MS1-based label-free quantification enables reproducible protein measurements by comparing precursor ion peaks across runs.
• MaxQuant (MQ) is a widely used platform, while Proteome Discoverer (PD) recently introduced its Minora tool for MS1 quantification.

Purpose of the Study:

• To comparatively evaluate six MS1-based quantification methods from MQ and PD.
• To assess quantification yield, dynamic range, reproducibility, accuracy, sensitivity, and specificity across various simulated proteomics scenarios.

Main Methods:

• Measured precursor ion peak intensity (MQ, PD) and area (PD only).
• Applied quantification methods with and without normalization.
• Utilized simulated datasets covering diverse protein abundance ratios and amounts.

Main Results:

• PD generally outperformed MQ in quantification yield, dynamic range, and reproducibility.
• PD methods with normalization showed superior accuracy and sensitivity for abundance ratio estimation, especially in narrow ranges.
• MQ methods exhibited slightly higher specificity, accuracy, and precision; optimized log ratio thresholds improved these metrics for both platforms.

Conclusions:

• PD offers advantages over MQ for MS1-based label-free quantification, particularly with normalization.
• Neither platform achieved fully satisfactory measurements in low-abundance ranges.
• Optimized log ratio thresholds are crucial for maximizing performance metrics, aiding researchers in selecting appropriate quantification strategies.