Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition

Motivation: Chemical cross-linking coupled to mass spectrometry (XLMS) emerged as a powerful technique for studying protein structures and large-scale protein-protein interactions. Nonetheless, XLMS lacks software tailored toward dealing with multiple conformers; this scenario can lead to high-quality identifications that are mutually exclusive. This limitation hampers the applicability of XLMS in structural experiments of dynamic protein systems, where less abundant conformers of the target protein are expected in sample. Results: We present QUIN-XL, a software that uses unsupervised clustering to group cross-link identifications by their quantitative profile across multiple samples. QUIN-XL highlights regions of the protein or system presenting changes in its conformation when comparing different biological conditions. We demonstrate the usefulness of our software by revisiting the HSP90 protein, comparing three of its different conformers. QUIN-XL’s clusters correlate directly to known protein 3D structures of the conformers and therefore validates our software.