MSstatsBioNet

MSstatsBioNet provides network analysis tools for mass spectrometry-based proteomics data by integrating MSstats differential abundance results with biological network databases for enrichment analysis and visualization.

Key Features:

• MSstats Integration: The package accepts the output of MSstats differential abundance analysis as input for downstream network analysis.
• Enrichment Analysis: The package provides functions to perform enrichment analysis in the context of prior knowledge from past literature.
• Network Visualization: The package provides functions for visualization of proteomics data in the context of biological networks.
• INDRA Database Integration: The package integrates with INDRA, a database of biological networks extracted from the literature using text mining techniques.

Scientific Applications:

• Proteomics Network Analysis: MSstatsBioNet enables network-based interpretation of mass spectrometry-based proteomics differential abundance results using prior knowledge from published literature.

Methodology:

The package takes as input the output of MSstats differential abundance analysis and integrates with INDRA, a database of biological networks extracted from the literature using text mining techniques.