PXD011931

PXD011931 is an original dataset announced via ProteomeXchange.

Title	PhoX - An IMAC-enrichable Crosslinking Reagent
Description	Chemical crosslinking mass spectrometry is rapidly emerging as a prominent technique to study protein structures. Structural information is obtained by covalently connecting peptides in close proximity by small reagents and identifying the resulting peptide pairs by mass spectrometry. However, sub-stoichiometric reaction efficiencies render routine detection of crosslinked peptides problematic. Here we present a new tri-functional crosslinking reagent, termed PhoX, which is decorated with a stable phosphonic acid handle. This makes the crosslinked peptides amenable to the well-established IMAC enrichment. The handle allows for 300x enrichment efficiency and 97% specificity, dramatically reducing measurement time and improving data quality. We exemplify the approach on various model proteins and protein complexes, e.g. resulting in a structural model of LRP1/RAP complex. PhoX is also applicable to whole cell lysates. When focusing the database search on ribosomal proteins, our first attempt resulted in 355 crosslinks, out-performing current efforts in less measurement time.
HostingRepository	PRIDE
AnnounceDate	2023-05-15
AnnouncementXML	Submission_2023-05-15_02:19:20.990.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	RichardScheltema
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2018-12-04 07:13:06	ID requested
1	2019-09-13 09:46:48	announced
2	2019-10-25 05:22:39	announced	2019-10-25: Updated publication reference for PubMed record(s): 31572778.
3	2023-05-15 02:18:16	announced	2023-05-15: Updated project metadata.
⏵ 4	2023-05-15 02:19:21	announced	2023-05-15: Updated project metadata.

Steigenberger B, Pieters RJ, Heck AJR, Scheltema RA, PhoX: An IMAC-Enrichable Cross-Linking Reagent. ACS Cent Sci, 5(9):1514-1522(2019) [pubmed]

ProteomeXchange project tag: EPIC-XS

submitter keyword: phosphonic acid, XlinkX,Tri-functional crosslinker, structural biology, crosslinking mass spectrometry, IMAC enrichable crosslinker

RichardScheltema
contact affiliation	Biomolecular Mass Spectrometry Pharmaceutical Sciences Utrecht University
contact email	r.a.scheltema@uu.nl
lab head
RichardScheltema
contact affiliation	Utrecht University
contact email	r.a.scheltema@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/2019/09/PXD011931

PRIDE project URI

• PRIDE
  1. PXD011931
     1. Label: PRIDE project
     2. Name: PhoX - An IMAC-enrichable Crosslinking Reagent