PXD005079

PXD005079 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Estimate phosphopeptide identification rate by tandem mass spectrometry
Description	Mass spectrometry has played a significant role in the identification of unknown phosphoproteins and sites of phosphorylation in biological samples. Analysis of protein phosphorylation, in particular large scale phosphorylation analysis – phosphoproteomics, has recently been enhanced by efficient enrichment, fast and accurate instrument, and better software, but challenges remain because of low stoichiometry of phosphorylation and poor efficiency in ionization and fragmentation due to neutral loss. To evaluate current mass spectrometric performance, we present here a method to estimate phosphopeptide identification efficiency by tandem mass spectrometry. Phosphopeptides were directly isolated from whole plant cell extracts, dephosphorylated, and then incubated with three purified kinases, CK2, MAPK6, and SnRK2.6, along with 16O4- and 18O4-ATP separately, for in vitro kinase reactions. Phosphopeptides were further enriched and analyzed by LC-MS. Phosphopeptide identification rate was estimated by comparing phosphopeptides identified by tandem mass spectrometry with phosphopeptide pairs generated by stable isotope labeled kinase reactions. Overall we found that the current high speed and high accurate mass spectrometry can only identify 20-40% of total phosphopeptides mainly due to relatively poor fragmentation and low abundance.
HostingRepository	jPOST
AnnounceDate	2016-10-02
AnnouncementXML	Submission_2022-09-18_03:34:10.909.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chuan-Chih Hsu
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	S-carboxamidomethyl-L-cysteine; O-phospho-L-threonine; O-phospho-L-serine; O4'-phospho-L-tyrosine; L-methionine sulfoxide; alpha-amino acetylated residue; unknown modification
Instrument	LTQ Orbitrap Velos

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2016-10-01 14:45:29	ID requested
1	2016-10-01 14:45:32	announced
2	2018-09-18 23:35:23	announced	Updated CV, FTP location and Modification list.
3	2021-02-04 16:41:23	announced	2021-02-04: Updated FTP location.
⏵ 4	2022-09-18 03:34:11	announced	2022-09-18: Updated FTP location.

Publication List

Dataset with its publication pending

Dataset with its publication pending

Keyword List

submitter keyword: Phosphopeptide identification rate, Mass spectrometry, Kinase reaction

submitter keyword: Phosphopeptide identification rate, Mass spectrometry, Kinase reaction

Contact List

Dr. W. Andy Tao
lab head
Chuan-Chih Hsu
contact affiliation	Purdue University
dataset submitter

Full Dataset Link List

jPOST dataset URI
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.jpostdb.org/JPST000196/

jPOST dataset URI

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.jpostdb.org/JPST000196/