Kojak

Kojak analyzes cross-linked peptide mass spectra to identify cross-linked peptides and map protein–protein interactions and protein topologies.

Key Features:

• Spectral processing and scoring: Integrates spectral processing and scoring schemes derived from traditional database search algorithms to identify cross-linked peptides.
• Chemical cross-linker support: Supports a variety of chemical cross-linkers with or without heavy isotope labels.
• Cleavable cross-linker support: Includes support for cleavable cross-linkers to expand applicable experimental designs.
• Updated scoring metrics: Implements improved scoring metrics that enhance accuracy and sensitivity of cross-link identifications.
• Homomultimer identification: Identifies cross-links between ^15N-labeled homomultimers.
• Performance: Increases cross-link identification rates while reducing computational time relative to prior cross-linking algorithms.
• Integration with Trans-Proteomic Pipeline: Integrates with the Trans-Proteomic Pipeline and enables validation using PeptideProphet and iProphet.

Scientific Applications:

• Protein–protein interaction mapping: Identifies interacting sites within proteins from cross-linked peptide spectra.
• Protein topology and spatial restraints: Provides information on protein spatial orientation and topologies via fragmentation ion spectral analysis of cross-linked peptides.
• Structural proteomics: Supports characterization of protein complexes and structural analysis using chemical cross-linking data.
• Isotope-labeling studies: Applies to experiments involving heavy isotope labels and ^15N-labeled homomultimers.

Methodology:

Performs spectral processing and fragmentation-ion spectral analysis using scoring schemes from database search algorithms, incorporates updated scoring metrics, supports cleavable cross-linkers and ^15N homomultimer identification, and integrates results with the Trans-Proteomic Pipeline for validation by PeptideProphet and iProphet.