PXD040267-1

PXD040267 is an original dataset announced via ProteomeXchange.

Title	Light-induced orthogonal fragmentation of crosslinked peptides
Description	Crosslinking mass spectrometry provides pivotal information on the structure and interaction of proteins. MS-cleavable crosslinkers are regarded as a cornerstone for the analysis of complex mixtures. Yet they fragment under similar conditions as peptides, leading to mixed fragmentation spectra of the crosslinker and peptide. This hampers selecting individual peptides for their independent identification. Here we introduce orthogonal cleavage, using ultraviolet photodissociation (UVPD) to increase crosslinker over peptide fragmentation. We designed and synthesized a crosslinker that can be cleaved at 213 nm in a commercial mass spectrometer configuration. In an analysis of crosslinked E. coli lysate, the crosslinker-to-peptide fragment intensity ratio increases from nearly 1 for a conventionally cleavable crosslinker to 5 for the UVPD cleavable crosslinker. This largely increased the sensitivity of selecting the individual peptides for MS3, even more so with an improved doublet detection algorithm.
HostingRepository	PRIDE
AnnounceDate	2023-08-28
AnnouncementXML	Submission_2023-08-28_03:20:02.249.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD040267
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	LarsKolbowski
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-02-20 05:01:17	ID requested
⏵ 1	2023-08-28 03:20:02	announced
2	2023-11-14 07:17:31	announced	2023-11-14: Updated project metadata.
3	2024-10-22 06:02:01	announced	2024-10-22: Updated project metadata.

10.6019/PXD040267;

submitter keyword: CLMS, cleavable crosslinker, crosslinking, UVPD

JuriRappsilber
contact affiliation	Technische Universität Berlin, Chair of Bioanalytics, 10623 Berlin, Germany Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK Si-M/"Der Simulierte Mensch", a Science Framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, Berlin, Germany
contact email	juri.rappsilber@tu-berlin.de
lab head
LarsKolbowski
contact affiliation	TU Berlin
contact email	lars.kolbowski@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/2023/08/PXD040267

PRIDE project URI

• PRIDE
  1. PXD040267
     1. Label: PRIDE project
     2. Name: Light-induced orthogonal fragmentation of crosslinked peptides