PXD040103

PXD040103 is an original dataset announced via ProteomeXchange.

Title	Optimising complexome profiling for systematic exploration of DNA-/RNA-protein complexes in human mitochondria
Description	Here we aimed to improve native gel electrophoresis-based complexome profiling (CP) method for examination of mitochondrial (mt)DNA-/RNA-protein complexes. We compared the performance of Blue Native PAGE (BNE) and high resolution Clear Native PAGE (hrCNE). We found that hrCNE much better preserves the integrity of mtDNA-/RNA-protein complexes.To further improve the detection of mtDNA-binding proteins, we treated solubilized mitochondrial samples with DNase I prior to separation on hrCNE or BNE. To characterize the detected by hrCNE mtRNA-protein complexes, we performed CP with samples treated with RNase A. To validate the utility of the method, we performed CP using mitochondria isolated from cells treated with ethidium bromide as well as from cells recovering after this treatment. Our study not only helps to validate and unveil proteins involved in mitochondrial DNA- and RNA-related processes, but also offers a convenient and systematic way for analysing these interactions that can be used equally well for the investigation of the nucleus and other DNA-/RNA-containing cell compartments.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:00:09.336.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alisa Potter
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-02-13 10:30:57	ID requested
1	2023-08-11 14:32:34	announced
2	2023-11-14 06:43:27	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 06:00:09	announced	2024-10-22: Updated project metadata.

10.1093/NAR/GKAD697;

submitter keyword: mtDNA,Mitochondria, mass spectrometry, DNA-protein complex, native gel electrophoresis, RNA-protein complex, complexome profiling

Johannes N. Spelbrink
contact affiliation	Radboud Center for Mitochondrial Medicine, Department of Paediatrics, Radboudumc, Nijmegen, The Netherlands
contact email	Hans.Spelbrink@radboudumc.nl
lab head
Alisa Potter
contact affiliation	Radboudumc, Department of Paediatrics
contact email	potteralisa@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/2023/08/PXD040103

PRIDE project URI

• PRIDE
  1. PXD040103
     1. Label: PRIDE project
     2. Name: Optimising complexome profiling for systematic exploration of DNA-/RNA-protein complexes in human mitochondria