Limelight

Limelight provides data sharing, analysis, and visualization for mass spectrometry data from data-dependent acquisition (DDA) pipelines.

Key Features:

• Multi-format data import: Imports data from many widely used open-mass and closed-mass search software workflows.
• Native score retention: Uses the native scores from respective search workflows without re-scoring or modification.
• Complete data stack access: Provides access from raw and annotated scan data to peptide-spectrum matches, quality control, peptides, proteins, and modifications.
• Pipeline-independent operation: Supports data from any DDA workflow and is not tied to any specific software pipeline.

Scientific Applications:

• Proteome profiling: Analyzes protein expression across samples using DDA mass spectrometry data.
• Protein-protein interaction studies: Interprets mass spectrometry data from affinity purification and interaction experiments.
• Biomarker discovery: Supports identification and validation of protein biomarkers from mass spectrometry datasets.
• Protein modification analysis: Enables detection and interpretation of post-translational modifications from search results.

Methodology:

Limelight imports search results from common mass spectrometry search engines and preserves native scoring metrics for visualization and collaborative analysis.