PXD061764-1

PXD061764 is an original dataset announced via ProteomeXchange.

Title	Dynamic Organellar Mapping in yeast exposed to ER stress
Description	Sophisticated techniques are available for systematic studies of yeast cell biology. However, it remains challenging to investigate protein subcellular localization changes on a proteome-wide scale. Here, we apply Dynamic Organellar Maps (DOMs) by label-free mass spectrometry to detect localization changes of native, untagged proteins during endoplasmic reticulum (ER) stress. We find that hundreds of proteins shift between cellular compartments. For example, we show that numerous secretory pathway proteins accumulate in the ER, thus defining the extent and selectivity of ER retention of misfolded proteins. Furthermore, we identify candidate cargo proteins of the ER reflux pathway, determine constituents of reticulon clusters that segregate from the remainder of the ER and provide evidence for altered nuclear pore complex composition and nuclear import. These findings uncover protein relocalization as a major aspect of cellular reorganization during ER stress and establish DOMs as a powerful discovery tool in yeast. This dataset comprises the comparative experiment comparing untreated cells, with ones treated with either DTT or tunicamycin. The data analysis reveals a multitude of changes in a classical volcano analysis as well as in the multivariate outlier analysis of subcellular localization changes.
HostingRepository	PRIDE
AnnounceDate	2025-12-03
AnnouncementXML	Submission_2025-12-03_10:55:33.477.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Julia Schessner
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: NEWT:4932; scientific name: Saccharomyces cerevisiae; NCBI TaxID: NCBITaxon:4932;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-12 09:55:03	ID requested
⏵ 1	2025-12-03 10:55:33	announced

10.1038/S41467-025-66946-8;

submitter keyword: tunicamycin,Dynamic Organellar Maps, Yeast, ER stress, DTT, Subcellular localization

Georg H H Borner
contact affiliation	Department of Proteomics and Signal Transduction, Systems Biology of Membrane Trafficking Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany
contact email	borner@biochem.mpg.de
lab head
Julia Schessner
contact affiliation	Max-Planck-Institute of Biochemistry
contact email	schessner@biochem.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/2025/12/PXD061764

PRIDE project URI

• PRIDE
  1. PXD061764
     1. Label: PRIDE project
     2. Name: Dynamic Organellar Mapping in yeast exposed to ER stress