PXD001134

PXD001134 is an original dataset announced via ProteomeXchange.

Title	Sample preparation for phosphoproteomic analysis of circadian time series in Arabidopsis thaliana
Description	Systems biological approaches to study the Arabidopsis thaliana circadian clock have mainly focused on transcriptomics while little is known about the proteome, and even less about post-translational modifications. Evidence has emerged that post-translational protein modifications, in particular phosphorylation, play an important role for the clock and its output. Phosphoproteomics is the method of choice for a large scale approach to gain more knowledge about rhythmic protein phosphorylation. Recent plant phosphoproteomics publications have identified several thousand phosphopeptides. However, the methods used in these studies are very labour-intensive and therefore not suitable to apply to a well-replicated circadian time series. To address this issue, we present and compare different strategies for sample preparation for phosphoproteomics that are compatible with large numbers of samples. Methods are compared regarding number of identifications, variability of quantitation and functional categorization. We focus on the type of detergent used for protein extraction as well as methods for its removal. We also test a simple two-fraction separation of the protein extract.
HostingRepository	PRIDE
AnnounceDate	2016-07-08
AnnouncementXML	Submission_2016-07-08_06:52:43.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD001134
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Johanna Krahmer
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	monohydroxylated residue; acetylated residue; phosphorylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2014-07-15 02:31:21	ID requested
1	2016-07-08 06:48:33	announced
⏵ 2	2016-07-08 06:52:44	announced	Updated publication reference for PubMed record(s): 2566246, 25662467.

Krahmer J, Hindle MM, Martin SF, Le Bihan T, Millar AJ, Sample preparation for phosphoproteomic analysis of circadian time series in Arabidopsis thaliana. Methods Enzymol, 551():405-31(2015) [pubmed]

Jensen DB, Albrektsen SB, Krag C, Development of metastatic skin cancer during methotrexate therapy for psoriasis. Acta Derm Venereol, 69(3):274-5(1989) [pubmed]

curator keyword: Technical

submitter keyword: Arabidopsis thaliana, phosphoproteomics, phosphopeptide enrichment, detergent removal, fractionation, acid-labile detergent

Andrew John Millar, FRS
contact affiliation	SynthSys - Systems and Synthetic Biology University of Edinburgh
contact email	Andrew.Millar@ed.ac.uk
lab head
Johanna Krahmer
contact affiliation	University of Edinburgh
contact email	j.krahmer@sms.ed.ac.uk
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/2016/07/PXD001134

PRIDE project URI

• PRIDE
  1. PXD001134
     1. Label: PRIDE project
     2. Name: Sample preparation for phosphoproteomic analysis of circadian time series in Arabidopsis thaliana