PXD014359

PXD014359 is an original dataset announced via ProteomeXchange.

Title	Cross-linking mass spectrometry analysis of trimeric complex of CRM1, SNP1 and RanGTP cross-linked with BS3
Description	An X-ray crystallography structure of the trimeric nuclear export complex of CRM1, SNP1 and RanGTP is available on the PDB database with the ID 3GJX. To get an XL-MS dataset of a clean sample of a stable protein complex for benchmarking purposes, another sample from the protein expression, purification and complex assembly employed in the crystallography study was also cross-linked and analyzed by mass spectrometry. The tools OpenPepXL, pLink 2, Kojak, StavroX, XiSearch and xQuest were used to analyze this dataset with comparable search settings.
HostingRepository	PRIDE
AnnounceDate	2020-10-20
AnnouncementXML	Submission_2020-10-19_22:35:20.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Eugen Netz
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-06-24 06:38:46	ID requested
⏵ 1	2020-10-19 22:35:21	announced

Netz E, Dijkstra TMH, Sachsenberg T, Zimmermann L, Walzer M, Monecke T, Ficner R, Dybkov O, Urlaub H, Kohlbacher O, OpenPepXL: An Open-Source Tool for Sensitive Identification of Cross-Linked Peptides in XL-MS. Mol Cell Proteomics, 19(12):2157-2168(2020) [pubmed]

submitter keyword: Technical dataset

Oliver Kohlbacher
contact affiliation	Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany; Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Germany; Quantitative Biology Center (QBiC), University of Tübingen, Germany; Institute for Translational Bioinformatics, University Hospital Tübingen, Germany; Institute for Bioinformatics and Medical Informatics, University of Tübingen, Germany;
contact email	oliver.kohlbacher@uni-tuebingen.de
lab head
Eugen Netz
contact affiliation	Biomolecular Interactions, Max Planck Institute for Developmental Biology
contact email	eugen.netz@gmail.com
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/2020/10/PXD014359

PRIDE project URI

• PRIDE
  1. PXD014359
     1. Label: PRIDE project
     2. Name: Cross-linking mass spectrometry analysis of trimeric complex of CRM1, SNP1 and RanGTP cross-linked with BS3