PXD039754

PXD039754 is an original dataset announced via ProteomeXchange.

Title	RNxQuest: an extension to the xQuest pipeline enabling analysis of protein-RNA cross-linking/mass spectrometry data
Description	The recently introduced cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) technique enables protein-RNA cross-links to be used as precisely localized distance restraints in de novo structural modelling. The novel data type requires a bespoke data analysis approach. The new RNxQuest Python package supports this approach. Here we demonstrate the performance of the new package using a mixture of novel and published datasets.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_07:28:34.638.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christopher Sarnowski
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2023-02-01 03:52:37	ID requested
1	2023-09-06 01:05:22	announced
⏵ 2	2023-11-14 07:28:35	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: UV cross-linking

MBNL1

FOX1

PTBP1

BSA

cross-linking

XL-MS

structural proteomics

protein-RNA

RNA-protein

protein-RNA complex

RNA-protein complex

CLIR-MS

Alexander Leitner
contact affiliation	ETH Zurich, Institute of Molecular Systems Biology
contact email	leitner@imsb.biol.ethz.ch
lab head
Christopher Sarnowski
contact affiliation	Institute of Molecular Systems Biology, Department of Biology, ETH Zürich
contact email	sarnowski@imsb.biol.ethz.ch
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/2023/09/PXD039754

PRIDE project URI

• PRIDE
  1. PXD039754
     1. Label: PRIDE project
     2. Name: RNxQuest: an extension to the xQuest pipeline enabling analysis of protein-RNA cross-linking/mass spectrometry data