PXD013083

PXD013083 is an original dataset announced via ProteomeXchange.

Title	Finding and using Diagnostic Ions in Collisional Induced Crosslinked Peptide Fragmentation Spectra
Description	Crosslinking mass spectrometry (XL-MS) has emerged as a powerful tool in its own right for the investigation of protein structures and interactions. Utilizing standard shotgun MS mass spectrometry equipment and specialized database search software, crosslinked peptide-pairs can be identified and directly translated into distance constraints for protein structure and protein-protein interaction investigations. Whereas the gas-phase dissociation behavior of linear peptides is well understood, less is however known about the gas-phase dissociation behavior of crosslinked peptides. In this work, we set out to expose the behavior of commonly used crosslinking reagents, both non- as well as gas-phase cleavable, using synthetic peptides to establish mechanistic insights. We describe that crosslinked peptide pairs generate specific fragmentation patterns under HCD and CID fragmentation conditions, distinct from mono-linked peptide and non-modified peptides. We discuss in detail the resulting diagnostic ions that can help distinguishing linear peptides from mono-linked and crosslinked peptide pairs and how that may be used to further increase the efficiency of XL-MS analysis.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_07:01:26.553.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Barbara Steigenberger
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-03-13 06:55:16	ID requested
1	2019-07-16 02:38:00	announced
2	2019-12-13 04:20:21	announced	2019-12-13: Updated publication reference for DOI(s): 10.1016/j.ijms.2019.116184.
⏵ 3	2023-11-14 07:01:27	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: XlinkX,Crosslinking mass spectrometry, gas phase fragmentation of crosslinks

Albert A.J.R. Heck
contact affiliation	Netherlands Proteomics Centre, Biomolecular Mass Spectrometry and Proteomics
contact email	A.J.R.Heck@uu.nl
lab head
Barbara Steigenberger
contact affiliation	Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University
contact email	B.A.Steigenberger@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/2019/07/PXD013083

PRIDE project URI

• PRIDE
  1. PXD013083
     1. Label: PRIDE project
     2. Name: Finding and using Diagnostic Ions in Collisional Induced Crosslinked Peptide Fragmentation Spectra