PXD033409

PXD033409 is an original dataset announced via ProteomeXchange.

Title	Xlink Mapping and AnalySis (XMAS) - Crosslinking study of commercial human Fibrinogen
Description	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.
HostingRepository	PRIDE
AnnounceDate	2022-05-06
AnnouncementXML	Submission_2022-05-06_04:00:43.185.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Pascal Albanese
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-04-24 12:21:17	ID requested
⏵ 1	2022-05-06 04:00:43	announced

Dataset with its publication pending

submitter keyword: XL-MS, Phox, DSSO, DSS, Fibrinogen, Crosslinking

Richard Scheltema
contact affiliation	Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
contact email	r.a.scheltema@uu.nl
lab head
Pascal Albanese
contact affiliation	Utrecht University
contact email	p.albanese@uu.nl
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/05/PXD033409

PRIDE project URI

• PRIDE
  1. PXD033409
     1. Label: PRIDE project
     2. Name: Xlink Mapping and AnalySis (XMAS) - Crosslinking study of commercial human Fibrinogen