PXD019127-2

PXD019127 is an original dataset announced via ProteomeXchange.

Title	PhosR enables processing and functional analysis of phosphoproteomic data
Description	Mass spectrometry-based phosphoproteomics has transformed our ability to profile phosphorylation-based signalling in tissues and cells on a global scale. To infer the action of kinases and signalling pathways in phosphoproteomic experiments, we present PhosR, a set of tools and methodologies implemented in a suite of R packages for the comprehensive analysis of phosphoproteomic data. By applying to both published and new phosphoproteomic datasets, we illustrate PhosR in data imputation and normalisation using a novel set of ‘stably phosphorylated sites’ and in functional analysis for inferring kinase activities and signalling pathways. In particular, we introduce a ‘signalome’ construction method for identifying a collection of signalling modules that allow us to summarise and visualise the interaction of kinases and their collective action on signal transduction. Together, our data and findings demonstrate the utility of PhosR in processing and generating novel biological knowledge from MS-based phosphoproteomic data.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:17:44.612.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Taiyun Kim
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	phosphorylated residue; monohydroxylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-05-12 05:59:37	ID requested
1	2021-01-12 23:57:09	announced
⏵ 2	2024-10-22 05:17:45	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: phosphoproteomics, preprecessing, batch correction, mass-spectrometry, signalome, kinase-substrate relationship, imputation

Pengyi Yang
contact affiliation	School of Mathematics and Statistics, The University of Sydney
contact email	pengyi.yang@sydney.edu.au
lab head
Taiyun Kim
contact affiliation	The University of Sydney
contact email	taiyun.kim@sydney.edu.au
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/2021/01/PXD019127

PRIDE project URI

• PRIDE
  1. PXD019127
     1. Label: PRIDE project
     2. Name: PhosR enables processing and functional analysis of phosphoproteomic data