MeroX

MeroX identifies protein-protein cross-links from MS/MS data generated with MS-cleavable reagents to derive spatial constraints for structural proteomics studies.

Key Features:

• Automated analysis: Automates screening and assignment of characteristic fragment ions from MS/MS spectra of cleavable cross-linkers.
• Fragment ion pattern recognition: Utilizes doublet fragmentation patterns produced by MS-cleavable cross-linkers such as DSBU, DSSO, CDI, and PIR linkers to distinguish cross-link types and enable identification without requiring MS(3).
• File and instrument compatibility: Supports a range of data file formats and is compatible with mass spectrometers that acquire MS/MS data.
• False discovery rate calculation: Computes false discovery rates to provide high-confidence scoring of identified cross-links.
• Integrated experimental workflow support: Supports workflows encompassing protein cross-linking with MS-cleavable reagents, enzymatic digestion, enrichment by strong cation-exchange chromatography (SCX), and LC/MS/MS analysis.
• Large dataset handling: Designed to process large datasets efficiently for routine proteomics analyses.

Scientific Applications:

• Structural proteomics: Derives spatial restraints for characterization of three-dimensional structures of protein assemblies and mapping protein-protein interactions.
• Model systems and complexes: Applied to purified proteins such as BSA, large complexes such as the Escherichia coli ribosome, and specific interactions (e.g., calmodulin with Munc13 peptide).

Methodology:

Automated assignment of characteristic MS/MS fragment ions from MS-cleavable cross-linkers using doublet pattern recognition, identification of cross-links without MS(3), and false discovery rate calculation for scoring.