Comet

Comet performs tandem mass spectrometry (MS/MS) sequence database searches to identify peptides and proteins from experimental spectra.

Key Features:

• MS/MS sequence database searching: Performs sequence database searches using tandem mass spectrometry (MS/MS) data against protein sequence databases.
• SEQUEST-derived algorithm: Implements scoring and matching algorithms derived from the academic SEQUEST search engine.
• Theoretical spectrum generation: Generates theoretical spectra from protein sequences for peptide-spectrum matching.
• Peptide-spectrum matching and scoring: Compares experimental MS/MS spectra to theoretical spectra and ranks peptide-spectrum matches using scoring algorithms.
• Peptide and protein identification: Identifies peptides and infers proteins present in a sample based on matched spectra.

Scientific Applications:

• Peptide and protein identification: Identifying peptides and proteins from tandem MS/MS data in proteomics studies.
• Proteome characterization: Supporting discovery of protein functions and interactions through large-scale MS/MS database searches.
• Post-translational modification analysis: Enabling detection and analysis of protein modifications via matched MS/MS spectra.

Methodology:

Compares experimental MS/MS spectra against theoretical spectra generated from a protein sequence database and ranks peptide-spectrum matches using algorithms derived from SEQUEST.