MSstats

MSstats performs statistical relative quantification of proteins and peptides from mass spectrometry-based proteomics data, supporting label-free and label-based workflows and acquisition methods including data-dependent, targeted, and data-independent approaches.

Key Features:

• Flexible Statistical Modeling: Employs a family of linear mixed models to analyze identified and quantified spectral peaks for robust differential abundance inference.
• Workflow and Acquisition Support: Handles label-free and label-based experimental workflows and spectral acquisition methods including data-dependent acquisition (DDA), targeted acquisition, and data-independent acquisition (DIA).
• Comprehensive Output: Produces lists of differentially abundant peptides and proteins and summaries of relative abundances at peptide and protein levels.

Scientific Applications:

• Differential Abundance Analysis: Performs statistical testing for differential peptide and protein abundance across experimental conditions.
• Biomarker Discovery: Supports identification of candidate biomarkers through quantitative comparisons of peptide and protein abundance.
• Disease Mechanism Investigation: Facilitates investigation of disease mechanisms by quantifying proteomic changes.
• Pathway and Systems-level Analysis: Enables exploration of biological pathways via comparative proteomic quantification.

Methodology:

MSstats applies linear mixed models to identified and quantified spectral peaks, modeling fixed and random effects to account for variability in mass spectrometry data.