compomics-rover

compomics-rover provides visualization and validation support for quantitative mass spectrometry proteomics datasets to assist identification and manual validation of regulated proteins.

Key Features:

• Integration with Multiple Data Sources: Accepts quantitative data from proteomic analysis tools such as MASCOT Distiller and MaxQuant.
• Visualization of Quantitative Proteomics Data: Visualizes quantitative mass spectrometry-derived proteomics data to support inspection and interpretation of experimental results.
• Facilitation of Protein Regulation Validation: Supports selection and manual validation of algorithm-suggested regulated proteins within the dataset, addressing the protein inference problem.
• Contextual Analysis: Enables validation and assessment of regulated proteins within the context of the entire experimental dataset to inform regulation calls.

Scientific Applications:

• Quantitative Proteome Studies: Validation and inspection of regulated proteins identified in large-scale MS-based quantitative proteomics experiments.
• Biomarker Discovery and Disease Research: Support for manual validation of candidate regulated proteins used in biomarker and disease-related studies.
• Systems Biology: Assessment of proteomic regulation within whole-experiment context to support systems-level interpretation.

Methodology:

Integration of quantitative data from diverse analytical platforms into a unified visualization environment and selection/validation of regulated proteins within the full experimental dataset, addressing the protein inference problem.