xQuest

xQuest analyzes chemical cross-linking mass spectrometry (XL-MS) data to identify cross-linked peptides and derive distance restraints for structural characterization of proteins and protein complexes.

Key Features:

• Integration with XL-MS Data: Processes XL-MS data generated using disuccinimidyl suberate, a homobifunctional lysine-reactive cross-linking reagent.
• Peptide Enrichment (SEC): Supports analysis of cross-linked peptides enriched by peptide size-exclusion chromatography (SEC) to reduce non-cross-linked peptide interference.
• Tandem Mass Spectrometry Analysis: Analyzes tandem mass spectrometry (MS) data to detect spectra corresponding to cross-linked peptides.
• Cross-link Identification and Restraints: Identifies cross-links from MS data and reports distance restraints and spatial relationships among protein subunits.
• Integration with xProphet: Integrates with xProphet to enhance the reliability and accuracy of cross-link identification.

Scientific Applications:

• Structural Biology: Provides distance restraints for integrative modeling and structural interpretation of proteins and protein complexes.
• Protein Complex Characterization: Maps cross-links to elucidate the composition and architecture of protein complexes and subunit spatial organization.

Methodology:

xQuest processes tandem MS data to identify cross-linked peptides and derive distance restraints and can be used in conjunction with xProphet to validate cross-link assignments.