SIM-XL

SIM-XL identifies covalently cross-linked peptides from tandem mass spectrometry data to support structural characterization of proteins and protein complexes.

Key Features:

• Search-space reduction paradigm: Implements a search-space reduction approach that decreases candidate peptide-pair combinations to increase identification speed and sensitivity.
• Reporter ion utilization: Leverages reporter ions to select tandem mass spectra originating from cross-linked peptides, improving selection specificity for identification.
• 2D interaction map: Generates a two-dimensional interaction map to visualize protein-protein interactions inferred from cross-links.
• Spectrum-annotation tool: Performs annotation of tandem mass spectra for cross-linked peptides to support interpretation of fragment ions.
• Performance benchmarking: Demonstrated higher sensitivity and faster processing than competing tools on datasets including human HSP90.
• Data format support: Supports XL data in the mzIdentML format and references ProteomeXchange dataset PXD001677.

Scientific Applications:

• Structural characterization of proteins and protein complexes: Maps residue-residue proximities and protein-protein interactions from chemical cross-linking tandem mass spectrometry data.
• Cross-linking MS data analysis and benchmarking: Enables sensitive and rapid identification of cross-linked peptides for comparative analysis of datasets such as human HSP90.

Methodology:

Applies a search-space reduction paradigm, uses reporter ion detection to select tandem mass spectra, performs spectrum annotation, generates 2D interaction maps, and supports mzIdentML-formatted XL data.