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Xlink Mapping and AnalySis (XMAS) - Crosslinking study of commercial human Fibrinogen

ABSTRACT: Here, we introduce XMAS, a bundle that allows users to load results from several XL-MS search engines directly into ChimeraX and map the information onto protein structures. Besides automatically locating distance constraints on protein structures, XMAS offers the possibility to work with replicate experiments and/or different crosslinkers, and filter this data based on how many replicates for which a given distance constraint was detected, thereby increasing the data quality. Additionally, we introduce the concept of self-links, which allows easy modeling of homo-dimeric interactions. Core functionality is extended by the implementation of seamless connections to the HADDOCK suite to streamline otherwise time-consuming tasks in structural modeling pipelines. We then demonstrate these key elements of the XMAS bundle by modeling crosslinking data obtained from human fibrin clots. This software is freely available from the ChimeraX toolshed, with an extensive user manual and example datasets.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma

SUBMITTER: Pascal Albanese

LAB HEAD: Richard Scheltema

PROVIDER: PXD033409 | Pride | 2022-05-06

REPOSITORIES: Pride

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			Action	DRS
	20210430_L1_UM5_Steve021_SA_ID1_7_01.raw	Raw
	20210430_L1_UM5_Steve021_SA_ID1_8_01.raw	Raw
	20210430_L1_UM5_Steve021_SA_ID1_9_01.raw	Raw
	20210702_L1_UM5_alban001_SA_EXT00_Ilse_fbn_dss1_250mm_inj2.raw	Raw
	20210702_L1_UM5_alban001_SA_EXT00_Ilse_fbn_dss1_450mm_inj2.raw	Raw

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