PXD010919

PXD010919 is an original dataset announced via ProteomeXchange.

Title	Protein Complex identification and quantitative complexome by CN-PAGE
Description	The majority of cellular processes are carried out by protein complexes. Various size fractionation methods have previously been combined with mass spectrometry to identify protein complexes. However, most of these approaches lack the quantitative information which is required to understand how changes of protein complex abundance and composition affects metabolic fluxes. In this paper we present a proof of concept approach to quantitatively study the complexome in the model plant Arabidopsis thaliana at the end of the day (ED) and the end of the night (EN). We show that size-fractionation of native protein complexes by Clear-Native-PAGE (CN-PAGE), coupled with mass spectrometry can be used to establish abundance profiles along the molecular weight gradient. Furthermore, by deconvoluting complex protein abundance profiles, we were able to drastically improve the clustering of protein profiles. To identify putative interaction partners, and ultimately protein complexes, our approach calculates the Euclidian distance between protein profile pairs. Acceptable threshold values are based on a cut-off that is optimized by a receiver-operator characteristic (ROC) curve analysis. Our approach shows low technical variation and can easily be adapted to study in the complexome in any biological system.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:06:09.320.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Michal Gorka
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-08-28 23:15:00	ID requested
1	2019-11-12 13:40:30	announced
⏵ 2	2024-10-22 04:06:12	announced	2024-10-22: Updated project metadata.

10.1038/s41598-019-47829-7;

Gorka M, Swart C, Siemiatkowska B, Mart, í, nez-Jaime S, Skirycz A, Streb S, Graf A, Protein Complex Identification and quantitative complexome by CN-PAGE. Sci Rep, 9(1):11523(2019) [pubmed]

curator keyword: Biological

submitter keyword: CN-PAGE, mass spectrometry,Proteomics, protein complexes, protein-protein interactions

Alexander Graf
contact affiliation	Max Planck Institute of Molecular Plant Physiology Am Mühlenberg 1, 14476 Golm Germany
contact email	graf@mpimp-golm.mpg.de
lab head
Michal Gorka
contact affiliation	Max Planck Institute for Molecular Plant Physiology | Celon Pharma
contact email	gorka@mpimp-golm.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/2019/11/PXD010919

PRIDE project URI

• PRIDE
  1. PXD010919
     1. Label: PRIDE project
     2. Name: Protein Complex identification and quantitative complexome by CN-PAGE