PXD003643

PXD003643 is an original dataset announced via ProteomeXchange.

Title	Blind testing cross-linking/mass spectrometry under the auspices of the 11th critical assessment of methods of protein structure prediction (CASP11)
Description	We report the first blind test on the readiness of combining high-density cross-linking/mass spectrometry data in conjunction with ab initio structure prediction, through the help of Critical Assessment of protein Structure Prediction (CASP). This blind test was coordinated by the CASP organizers and utilized the experimental protocol developed in our lab for providing high-density cross-linking/mass spectrometry data in a matter of days. The CASP organizing committee identified and acquired suitable targets and published resulting data on the CASP web page for the community of structure predictors. We provided high-density cross-linking/mass spectrometry data for four targets in CASP11, revealing to us some of the current limitations of cross-linking. These are areas where the method must now develop. With CASP taking place biannually into the future, blind testing low-resolution structure analysis tools is a worthwhile and feasible undertaking.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:10:14.440.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Adam Belsom
SpeciesList	scientific name: Bacteroides caccae; NCBI TaxID: 47678; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Staphylococcus aureus; NCBI TaxID: 1280; scientific name: Ruminococcus gnavus; NCBI TaxID: 33038;
ModificationList	iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2016-02-16 02:11:40	ID requested
1	2016-12-02 01:18:06	announced
2	2019-02-12 08:03:21	announced	Updated publication reference for PubMed record(s): 28317030.
⏵ 3	2024-10-22 04:10:15	announced	2024-10-22: Updated project metadata.

Belsom A, Schneider M, Fischer L, Mabrouk M, Stahl K, Brock O, Rappsilber J, critical assessment of methods of protein structure prediction (CASP11). Wellcome Open Res, 1():24(2016) [pubmed]

10.12688/wellcomeopenres.10046.1;

curator keyword: Technical

submitter keyword: CASP, protein structure prediction,Cross-linking/mass spectrometry

Juri Rappsilber
contact affiliation	1. University of Edinburgh, Wellcome Trust Centre for Cell Biology, Edinburgh, United Kingdom. 2. Technische Universität Berlin, Institute of Biotechnology, Department of Bioanalytics, Berlin, Germany.
contact email	juri.rappsilber@ed.ac.uk
lab head
Adam Belsom
contact affiliation	Technische Universität Berlin
contact email	adam.belsom@tu-berlin.de
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/2016/12/PXD003643

PRIDE project URI

• PRIDE
  1. PXD003643
     1. Label: PRIDE project
     2. Name: Blind testing cross-linking/mass spectrometry under the auspices of the 11th critical assessment of methods of protein structure prediction (CASP11)