pyXLMS

pyXLMS streamlines the intermediate step of connecting crosslink search engine results with down-stream analysis tools for crosslinking mass spectrometry data interpretation.

Key Features:

• Multi-engine input support: pyXLMS supports input from seven different crosslink search engines and the mzIdentML format of the HUPO Proteomics Standards Initiative.
• Built-in analysis functionality: pyXLMS provides aggregation, validation, annotation, filtering, and visualization functionality for crosslink data.
• Export compatibility: pyXLMS exports data to more than ten supported down-stream analysis tools and formats.

Scientific Applications:

• Protein-protein interaction analysis: pyXLMS enables identification of protein-protein interactions from crosslinking mass spectrometry data.
• In vivo protein structure analysis: pyXLMS facilitates gaining insight into the structures of proteins in vivo from crosslink identifications.
• Cross-platform workflow standardization: pyXLMS allows the same data analysis workflow to be applied across a variety of different search engines.

Methodology:

pyXLMS re-analyzes publicly available crosslink datasets with a variety of different search engines to demonstrate applicability.