PXD035029-2

PXD035029 is an original dataset announced via ProteomeXchange.

Title	The regulatory landscape of the yeast phosphoproteome – ultra-deep reference phosphoproteomic DDA data
Description	We systematically exposed the yeast Saccharomyces cerevisiae to a wide array of 101 perturbations and generated a quantitative mass spectrometry-based atlas of early phosphoproteomic responses. Perturbations covered broad classes of environmental, chemical, and drug perturbations and systematically targeted diverse aspects of yeast cell biology. Importantly, most perturbations focused on capturing early signaling responses (5 min treatments). An ultra-deep yeast phosphoproteome was generated from a pooled sample of all 5 min perturbations by multi protease digestion, deep offline fractionations using two different peptide separation methods, and data-dependent acquisition (DDA). This submission includes 120 DDA-MS raw files that were used to generate a deep yeast phosphoproteome.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:01:50.877.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD035029
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Mario Leutert
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse; Orbitrap Exploris 480; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-30 07:17:51	ID requested
1	2023-08-27 09:50:30	announced
⏵ 2	2024-10-22 06:01:51	announced	2024-10-22: Updated project metadata.

10.6019/PXD035029;

submitter keyword: Signaling,Phosphoproteomics, Orbitrap Exploris 480, Orbitrap Eclipse, PTM, Saccharomyces cerevisiae, Stress Response, DDA, Phosphorylation, Phosphatase, Budding Yeast, Fractionation, R2-P2, Kinase

Judit Villén
contact affiliation	Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
contact email	jvillen@uw.edu
lab head
Mario Leutert
contact affiliation	Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
contact email	marioleutert@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/PXD035029

PRIDE project URI

• PRIDE
  1. PXD035029
     1. Label: PRIDE project
     2. Name: The regulatory landscape of the yeast phosphoproteome – ultra-deep reference phosphoproteomic DDA data