PXD003737-1

PXD003737 is an original dataset announced via ProteomeXchange.

Title	An optimised fragmentation regime for cross-linking/mass spectrometry
Description	In this study we compared three different fragmentation techniques and two combined fragmentation schemes available on a novel tribrid mass spectrometer (Orbitrap Fusion Lumos, Themro Fisher Scientific) CID, HCD, ETD, ETD with supplemental CID (ETciD) and ETD with supplemental HCD (EThcD) on cross-linked peptides obtained by tryptic cleavage of SDA-cross-linked Human Serum Albumin (HSA). The three-dimensional structure of HSA has been resolved by X-ray crystallography [35] and is used as ground-truth to evaluate the identification results. Right choice of the fragmentation method allows increasing the number of identified linkage sites, increasing the sequence coverage of both linked peptides thereby reducing the second peptide problem, and increasing the precision of cross-link site calling.
HostingRepository	PRIDE
AnnounceDate	2016-08-02
AnnouncementXML	Submission_2016-08-02_06:36:43.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sven Giese
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-03-03 05:39:39	ID requested
⏵ 1	2016-08-02 06:36:44	announced

Giese SH, Belsom A, Rappsilber J, Optimized Fragmentation Regime for Diazirine Photo-Cross-Linked Peptides. Anal Chem, 88(16):8239-47(2016) [pubmed]

curator keyword: Technical

submitter keyword: Cross-linking, CID, HCD, ETD, EThcD, ETciD

Juri Rappsilber
contact affiliation	1. Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany, 2. Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom; ( lab head )
contact email	juri.rappsilber@tu-berlin.de
lab head
Sven Giese
contact affiliation	Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
contact email	sven.giese@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/2016/08/PXD003737

PRIDE project URI

• PRIDE
  1. PXD003737
     1. Label: PRIDE project
     2. Name: An optimised fragmentation regime for cross-linking/mass spectrometry