DEP2

DEP2 provides an integrated workflow for analysis of mass spectrometry (MS)-based proteomics data, including quality control, peptide-to-protein summarization, hypothesis-driven differential analysis, functional exploration, and visualization.

Key Features:

• Updated analysis workflow: Incorporates alternative approaches to accommodate diverse types of proteomics data within a unified workflow.
• Peptide-to-protein summarization: Summarizes peptide-protein relationships to support protein-level quantification from peptide-level MS data.
• Quality control: Performs quality-control procedures to assess and ensure integrity of MS-based proteomics datasets.
• Hypothesis-driven differential analysis: Provides a flexible differential analysis workflow to identify significant changes in protein and peptide levels across conditions.
• Biological function exploration: Integrates functional mining to connect quantitative proteomics results with biological annotations.
• Visualization: Produces advanced visualizations to aid interpretation of quantitative and functional results.

Scientific Applications:

• Proteome-wide differential analysis: Identification of proteins and peptides with significant abundance changes across experimental conditions.
• Peptide-to-protein quantification: Derivation of protein-level quantification from peptide-level MS measurements.
• Functional interpretation of quantitative proteomics: Linking differential results to biological functions and annotations via functional mining.
• Analysis of biological and clinical MS datasets: Application to complex biological and clinical mass spectrometry-based proteomics studies.

Methodology:

Computational steps explicitly include quality control of MS-based proteomics data, peptide-to-protein summarization, hypothesis-driven differential analysis, functional mining/biological function exploration, and generation of visualization outputs.