PXD034997-2

PXD034997 is an original dataset announced via ProteomeXchange.

Title	The regulatory landscape of the yeast phosphoproteome – quantitative proteomics DIA 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), with the reasoning that functional phosphorylation of specific substrates occurs rapidly following stimulation, but promiscuous phosphorylation and confounding changes in transcript and protein abundances takes place more slowly. Large-scale proteomics and phosphoproteomics was enabled by our recently developed R2-P2 (Rapid-Robotic Phosphoproteomics) sample preparation workflow in combination with DIA measurements. In parallel to phosphoproteomic measurements we performed total proteome measurements on the same samples for 30 selected perturbations. This submission includes 126 quantitative DIA-MS raw files that were used for the total proteome analysis.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:01:55.538.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mario Leutert
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-30 03:08:54	ID requested
1	2023-08-27 10:20:07	announced
⏵ 2	2024-10-22 06:01:55	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: Signaling, DIA, Orbitrap Exploris 480,Stress Response, Saccharomyces cerevisiae, Budding Yeast, R2-P2

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/PXD034997

PRIDE project URI

• PRIDE
  1. PXD034997
     1. Label: PRIDE project
     2. Name: The regulatory landscape of the yeast phosphoproteome – quantitative proteomics DIA data