PXD020014

PXD020014 is an original dataset announced via ProteomeXchange.

Title	"In-gel cross-linking mass spectrometry (IGX-MS) of proteins and protein complexes"
Description	Cross-linking mass spectrometry has developed into an important method to study protein structures and interactions. The in-solution cross-linking workflows involve time and sample consuming steps and do not provide sensible solutions for differentiating cross-links obtained from co-occurring protein oligomers, complexes, or conformers. Here we developed a cross-linking workflow combining blue native PAGE with in-gel cross-linking mass spectrometry (IGX-MS). This workflow circumvents steps, such as buffer exchange and cross-linker concentration optimization. Additionally, IGX-MS enables the parallel analysis of co-occurring protein complexes using only small amounts of sample. Another benefit of IGX-MS observed by experiments on GroEL and purified bovine heart mitochondria, is the substantial reduction of artificial over-length cross-links when compared to in-solution cross-linking. We next used IGX-MS to investigate the complement components C5, C6, and their hetero-dimeric C5b6 complex. The obtained cross-links were used to generate a refined structural model of the complement component C6, resembling C6 in its inactivated state. This finding shows that IGX-MS can be used to provide new insights into the initial stages of the terminal complement pathway.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:16:41.787.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Johannes Hevler
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	carbamoylated residue; monohydroxylated residue; acetylated residue
Instrument	Orbitrap Fusion Lumos; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-25 05:26:44	ID requested
1	2020-12-14 05:22:18	announced
2	2022-02-13 16:42:58	announced	2022-02-14: Updated project metadata.
⏵ 3	2024-10-22 05:16:42	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

ProteomeXchange project tag: EPIC-XS

submitter keyword: BN-PAGE/ Cross-linking/ Protein complexes/ Complement/ Protein modeling

Albert J. R Heck
contact affiliation	Utrecht University
contact email	A.J.R.Heck@uu.nl
lab head
Johannes Hevler
contact affiliation	Utrecht University
contact email	j.f.hevler@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/2020/12/PXD020014

PRIDE project URI

• PRIDE
  1. PXD020014
     1. Label: PRIDE project
     2. Name: "In-gel cross-linking mass spectrometry (IGX-MS) of proteins and protein complexes"