PXD010070

PXD010070 is an original dataset announced via ProteomeXchange.

Title	Cross-linking mass spectrometry analyses of three different kinetochore protein complexes (KMN, NDC80C, MIS12C) using an MS-cleavable cross-linker, BuUrBu (DSBU)
Description	In order to develop a simplified cross-linking mass spectrometry protocol, we applied one-step size-exclusion chromatography (SEC) for peptide purification after proteolysis with Lys-C and trypsin. Three benchmark protein complexes (KMN, NDC80C, MIS12C) from human kinetochore were cross-linked with an MS-cleavable cross-linker (BuUrBu). After proteolysis, digested peptides were purified with SEC omitting the step of C18 column to avoid loss of cross-linked peptides. Our protocol showed improvement of existing protocols, and we could successfully identify over 700 cross-links per experiment of each of the three protein complexes. We also observed that about half of the non-redundant cross-links were not lysine-lysine cross-links but cross-links between lysine and side chains with alcohols (serine, threonine, tyrosine).
HostingRepository	PRIDE
AnnounceDate	2019-04-01
AnnouncementXML	Submission_2019-04-01_01:18:36.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dongqing Pan
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-06-08 03:41:43	ID requested
⏵ 1	2019-04-01 01:18:37	announced

Pan D, Brockmeyer A, Mueller F, Musacchio A, Bange T, Simplified Protocol for Cross-linking Mass Spectrometry Using the MS-Cleavable Cross-linker DSBU with Efficient Cross-link Identification. Anal Chem, 90(18):10990-10999(2018) [pubmed]

curator keyword: Biological

submitter keyword: cross-linking MS, MS-cleavable cross-linker, BuUrBu, DSBU, MeroX, Q-Exactive, human, kinetochore, protein complex

Tanja Bange
contact affiliation	1. Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund 2. Department for Systems Chronobiology, Institute of Medical Psychology, LMU Munich, Goethe-Str. 31, 80336 Munich
contact email	tanja.bange@med.uni-muenchen.de
lab head
Dongqing Pan
contact affiliation	Department of Mechanistic Cell Biology, Max-Planck Institute of Molecular Physiology, 9 Otto-Hahn-Str. 11, 44227 Dortmund
contact email	dongqing.pan@mpi-dortmund.mpg.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/2019/04/PXD010070

PRIDE project URI

• PRIDE
  1. PXD010070
     1. Label: PRIDE project
     2. Name: Cross-linking mass spectrometry analyses of three different kinetochore protein complexes (KMN, NDC80C, MIS12C) using an MS-cleavable cross-linker, BuUrBu (DSBU)