Mango: A General Tool for Collision Induced Dissociation-Cleavable Cross-Linked Peptide Identification

Area of Science:

• Proteomics
• Structural Biology
• Biochemistry

Background:

• Chemical cross-linking coupled with mass spectrometry is a key technique for investigating protein structures and interactions.
• Identifying cross-linked peptides is challenging, often requiring specialized methods and non-standard workflows.
• Cleavable cross-linkers simplify analysis by separating peptide masses from precursor ions.

Purpose of the Study:

• To introduce Mango, an open-source software tool designed to streamline the analysis of data from cleavable cross-linking experiments.
• To enable whole proteome investigations of protein interactions using standard mass spectrometry instrumentation.

Main Methods:

• Development of Mango software for extracting precursor masses from chimeric spectra generated by cleavable cross-linkers.
• Utilizing high-resolution tandem mass spectrometry (MS/MS) compatible with standard mass spectrometers.
• Integration of Mango with traditional proteomics search engines for peptide pair identification.

Main Results:

• Mango effectively extracts precursor masses from chimeric spectra, simplifying downstream analysis.
• The software enables the identification of thousands of cross-linked peptide pairs within the Escherichia coli proteome.
• Whole proteome cross-linking studies are feasible using standard MS/MS instruments without specialized modifications.

Conclusions:

• Mango significantly simplifies the identification of cross-linked peptides, making large-scale studies more accessible.
• This software facilitates comprehensive proteome-wide investigations of protein interactions.
• Mango democratizes protein interaction studies by removing the need for specialized equipment or non-standard methodologies.