Sage

Sage matches tandem mass spectra to peptide sequences to identify and quantify peptides in proteomics studies.

Key Features:

• High Performance: Engineered for rapid processing, providing substantially faster spectrum-to-peptide matching while maintaining competitive accuracy.
• Scalability and Cloud Readiness: Scales to large datasets and is suitable for deployment on cloud computing resources for high-throughput proteomic studies.
• Database Search Engine: Implements a proteomics database search engine for matching tandem mass spectra with peptide sequences.
• Retention Time Prediction: Provides peptide retention time prediction to support identification and quantification workflows.
• False Discovery Rate (FDR) Control: Includes mechanisms for controlling FDR to ensure statistical robustness of identifications.
• Open Source and Permissive License: Distributed under a permissive open-source license, enabling code inspection and modification.

Scientific Applications:

• Protein Identification: Matches tandem mass spectra to peptides to enable identification of proteins in complex biological samples.
• Peptide Quantification: Supports quantification workflows to measure peptide and protein abundances from mass spectra.
• Retention Time Modeling: Uses predicted retention times to improve identification confidence and alignment across runs.
• Statistical Validation: Applies FDR control for statistically robust peptide-spectrum matches and reported identifications.

Methodology:

Implements a proteomics database search engine that employs advanced algorithms to match tandem mass spectra to peptide sequences, optimized for speed while maintaining accuracy.