PXD012174

PXD012174 is an original dataset announced via ProteomeXchange.

Title	The human phosphoproteome map based on PRIDE data
Description	This project contains raw data, intermediate files and results used to create the PRIDE human phosphoproteome map. The map is based on joint reanalysis of 110 publicly available human datasets. All relevant datasets were retrieved from the PRIDE database, and after manual curation, only assays that employed dedicated phospho-enrichment sample preparation strategies (e. g. metal oxide affinity chromatography, anti-P-Tyr antibodies, etc.) were included. Raw files were jointly processed with MaxQuant computational platform using standard settings (see Data Processing Protocol). In total, the joint analysis allowed identification of 252,189 phosphosites at 1% peptide spectrum match false discovery rate (PSM FDR) (MQ search results available in ‘txt-100PTM’ folder), of which 121,896 passed the additional 1% site localization FDR threshold (MQ search results available in ‘txt-001PTM’ folder).
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:51:38.289.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andrew Jarnuczak
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ FT; LTQ Orbitrap Velos; Q Exactive; LTQ Orbitrap; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2018-12-24 02:08:53	ID requested
1	2019-02-14 11:51:39	announced
2	2020-06-01 14:18:14	announced	2020-06-01: Updated publication reference for PubMed record(s): 31819260.
⏵ 3	2024-10-22 04:51:41	announced	2024-10-22: Updated project metadata.

Ochoa D, Jarnuczak AF, Vi, é, itez C, Gehre M, Soucheray M, Mateus A, Kleefeldt AA, Hill A, Garcia-Alonso L, Stein F, Krogan NJ, Savitski MM, Swaney DL, Vizca, í, no JA, Noh KM, Beltrao P, The functional landscape of the human phosphoproteome. Nat Biotechnol, 38(3):365-373(2020) [pubmed]

10.1038/s41587-019-0344-3;

ProteomeXchange project tag: deep learning, benchmarking, machine learning

submitter keyword: post translational modification, reanalysis, PTM, public data reuse,phosphorylation

Juan Antonio Vizcaino
contact affiliation	European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
contact email	juan@ebi.ac.uk
lab head
Andrew Jarnuczak
contact affiliation	EBI
contact email	andrew.at.astra@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/2019/02/PXD012174

PRIDE project URI

• PRIDE
  1. PXD012174
     1. Label: PRIDE project
     2. Name: The human phosphoproteome map based on PRIDE data