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

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Louise Ulrich Kurt

LAB HEAD: Paulo Costa Carvalho

PROVIDER: PXD022443 | Pride | 2025-01-03

REPOSITORIES: Pride

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			Action	DRS
	161206_HsP_90_1.raw	Raw
	161206_HsP_90_2.raw	Raw
	161206_HsP_90_ADP_1.raw	Raw
	161206_HsP_90_ADP_2.raw	Raw
	161206_HsP_90_ATPgS_1.raw	Raw

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