PXD000612

PXD000612 is an original dataset announced via ProteomeXchange.

Title	Ultra-deep human phosphoproteome reveals different regulatory nature of Tyr and Ser/Thr-based signaling
Description	Regulatory protein phosphorylation controls nearly every normal and pathophysiological signaling system in eukaryotic cells. Despite great advances in mass spectrometry based-proteomics, the total number, localization and site-specific stoichiometry of this post-translational modification (PTM) are unknown. Here we develop stringent experimental and computational workflow, capable of mapping more than 50,000 distinct phosphorylated peptides in a single human cancer cell line. Label-free quantitation determined very high stoichiometries in mitosis or growth factor signaling and more than three-quarters of cellular proteins were detected as phosphoproteins. The proportion of phospho-Tyr drastically decreases as coverage of the phosphoproteome increases, whereas Ser/Thr sites only saturate for technical reasons. Tyrosine phosphorylation is maintained at especially low stoichiometric levels in the absence of specific signaling events. Unexpectedly, it is statistically enriched on higher abundance proteins and this correlates with the substrate Km values of tyrosine kinases. Our data suggests that P-Tyr should be considered a functionally separate PTM of eukaryotic proteomes.
HostingRepository	PRIDE
AnnounceDate	2014-10-23
AnnouncementXML	Submission_2014-10-23_02:50:04.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mario Oroshi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2013-12-02 02:12:12	ID requested
1	2014-08-06 11:22:01	announced
2	2014-08-07 00:30:31	announced	Updated project metadata.
3	2014-09-04 03:48:18	announced	Updated project metadata.
⏵ 4	2014-10-23 02:50:05	announced	Updated project metadata.

Sharma K, D'Souza RC, Tyanova S, Schaab C, Wi, ś, niewski JR, Cox J, Mann M, Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling. Cell Rep, 8(5):1583-94(2014) [pubmed]

curator keyword: Biological

submitter keyword: HeLa, Ultradeep phosphoproteome, Mitosis, EGF

Matthias Mann
contact affiliation	Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry
contact email	mmann@biochem.mpg.de
lab head
Mario Oroshi
contact affiliation	Proteomics
contact email	oroshi@biochem.mpg.de
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/2014/08/PXD000612

PRIDE project URI

• PRIDE
  1. PXD000612
     1. Label: PRIDE project
     2. Name: Ultra-deep human phosphoproteome reveals different regulatory nature of Tyr and Ser/Thr-based signaling