PXD015575

PXD015575 is an original dataset announced via ProteomeXchange.

Title	Investigation of Proteomic and Phosphoproteomic Responses to Signaling Network Perturbations Reveals Functional Pathway Organizations in Yeast
Description	Governance of protein phosphorylation by kinases and phosphatases constitutes an essential regulatory network in eukaryotic cells. Network dysregulation leads to severe consequences and is often a key factor in disease pathogenesis. Previous studies revealed multiple roles for protein phosphorylation and pathway structures in cellular functions from different perspectives. We sought to understand the roles of kinases and phosphatases from a protein homeostasis point of view. Using a streamlined tandem mass tag (SL-TMT) strategy, we systematically measured proteomic and phosphoproteomic responses to perturbations of phosphorylation signaling networks in yeast deletion strains. Ours results emphasize the requirement for protein normalization for more complete interpretation of phosphorylation data. Functional relationships between kinases and phosphatases were characterized at both proteome and phosphoproteome levels in three ways: 1) gene ontology enrichment analysis, 2) ∆gene-∆gene correlation networks and 3) molecule covariance networks. This resource illuminates kinase and phosphatase functions and pathway organizations.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:58:22.145.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jiaming Li
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	phosphorylated residue
Instrument	Orbitrap Fusion Lumos; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2019-09-25 02:01:50	ID requested
1	2019-11-15 08:43:48	announced
2	2020-01-14 06:40:50	announced	2020-01-14: Updated publication reference for PubMed record(s): 31722220.
⏵ 3	2024-10-22 04:58:25	announced	2024-10-22: Updated project metadata.

10.1016/j.celrep.2019.10.034;

Li J, Paulo JA, Nusinow DP, Huttlin EL, Gygi SP, Investigation of Proteomic and Phosphoproteomic Responses to Signaling Network Perturbations Reveals Functional Pathway Organizations in Yeast. Cell Rep, 29(7):2092-2104.e4(2019) [pubmed]

submitter keyword: streamlined tandem mass tag strategy, proteomics, protein regulation network, multi-notch MS3, protein kinases and phosphatases, phosphoproteomics, phosphorylation signaling pathway organization, phosphorylation regulation network

Steven Gygi
contact affiliation	Department of Cell Biology, Harvard Medical School
contact email	steven_gygi@hms.harvard.edu
lab head
Jiaming Li
contact affiliation	Harvard Medical School
contact email	jiaming_li@hms.harvard.edu
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/PXD015575

PRIDE project URI

• PRIDE
  1. PXD015575
     1. Label: PRIDE project
     2. Name: Investigation of Proteomic and Phosphoproteomic Responses to Signaling Network Perturbations Reveals Functional Pathway Organizations in Yeast