PXD001675

PXD001675 is an original dataset announced via ProteomeXchange.

Title	Quantitative cross-linking/mass spectrometry reveals subtle protein conformational changes
Description	We have developed quantitative cross-linking/mass spectrometry (QCLMS) to interrogate conformational rearrangements of proteins in solution. Our workflow was tested using a structurally well-described reference system, the human complement protein C3 and its activated cleavage product C3b. We found that small local conformational changes affect the yields of cross-linking residues that are near in space while larger conformational changes affect the detectability of cross-links. Distinguishing between minor and major changes required robust analysis based on replica analysis and a label-swapping procedure. By providing workflow, code of practice and a framework for semi-automated data processing, we lay the foundation for QCLMS as a tool to monitor the domain choreography that drives binary switching in many protein-protein interaction networks.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:25:38.877.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zhuo Chen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-01-14 01:25:10	ID requested
1	2016-06-16 08:41:00	announced
⏵ 2	2024-10-22 04:25:44	announced	2024-10-22: Updated project metadata.

Chen ZA, Fischer L, Cox J, Rappsilber J, Quantitative Cross-linking/Mass Spectrometry Using Isotope-labeled Cross-linkers and MaxQuant. Mol Cell Proteomics, 15(8):2769-78(2016) [pubmed]

submitter keyword: Quantitative cross-linking/mass spectrometry

conformation changes

human C3

activation of complement system

Juri Rappsilber
contact affiliation	1. Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, UK 2. Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Germany
contact email	juri.rappsilber@ed.ac.uk
lab head
Zhuo Chen
contact affiliation	Technischen Universität Berlin
contact email	zhuo.chen@ed.ac.uk
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/2016/06/PXD001675

PRIDE project URI

• PRIDE
  1. PXD001675
     1. Label: PRIDE project
     2. Name: Quantitative cross-linking/mass spectrometry reveals subtle protein conformational changes