SILACtor

SILACtor analyzes Protein Interaction Reporter (PIR) cross-linked proteins to identify and map interpeptide relationships from mass spectrometry data for proteomic structural and interaction studies.

Key Features:

• Chromatographic Profile Matching: Uses chromatographic profile matching to align cross-linked complexes and released peptides and to estimate p-values for interaction assignments.
• Integration with Mascot Database Searching: Incorporates Mascot database search results from MS/MS analysis of released peptides to identify cross-linked peptide sequences.
• False Discovery Rate Control: Reports a low false discovery rate (2.2%) to provide confidence in identified interpeptide relationships.
• Handling Coeluting Peptides: Tracks peptides involved in multiple, coeluting interactions and identifies additional interpeptide relationships even with poor profile correlation.
• Global Mapping and Custom Analysis: Enables global mapping of all interpeptide relationships and supports customized subsequent analyses targeting specific peptides of interest.

Scientific Applications:

• Proteomics of Protein-Protein Interactions: Applied in proteomic studies to detect and map protein-protein interactions using PIR cross-linking and mass spectrometry.
• Analysis of Protein Complexes: Used to map interpeptide relationships within protein complexes, exemplified by analyses of human serum albumin.
• Structural and Functional Inference: Provides interpeptide spatial information that aids in elucidating protein topology, proximal residues, and functional interfaces.

Methodology:

PIR cross-linkers form labile bonds that are fragmented under low energy collision or photodissociation in a mass spectrometer, and SILACtor applies chromatographic matching and mathematical relationships to analyze the resulting peptides.