PXD000433

PXD000433 is an original dataset announced via ProteomeXchange.

Title	Quantitative phosphoproteomics of Phytophthora infestans life stages
Description	The oomycete Phytophthora infestans is the causal agent of late blight in potato and tomato. Since the underlying processes that govern pathogenicity and development in P. infestans are largely unknown, we have performed a large-scale phosphoproteomics study of six different P. infestans life stages. We have obtained quantitative data for 2922 phosphopeptides and compared their abundance in different life stages. The samples were analysed on an LTQ Orbitrap XL ETD, operated in data dependent mode to automatically perform Orbitrap-MS and LTQ-MS/MS analysis. The raw data from the Orbitrap was converted to .mgf files using ProteoWizard. The Proteios software environment was used to search the mgf files with Mascot version 2.3.01 against a database consisting of all P. infestans proteins in UniProt as of 2010-04-22, concatenated with an equal size decoy database (random protein sequences with conserved protein length and amino acid distribution, in total 36,512 target and decoy protein entries). Search tolerances were set to 7 ppm for MS and 0.5 Da for MS/MS. One missed cleavage was allowed. Carbamidomethylation of cysteine residues was selected as a fixed modification and oxidation of methionine residues and phosphorylation of serine, threonine and tyrosine residues were selected as variable modifications. Search results were exported from Mascot as XML, including query level results, with a modification to the export script to include protein accession numbers also for the query (spectrum) level results. All search results, including the top ranked peptide for each spectrum, were imported to Proteios, where q values were calculated using the target-decoy method.
HostingRepository	PRIDE
AnnounceDate	2014-07-28
AnnouncementXML	Submission_2014-07-28_00:45:59.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000433
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Svante Resjo
SpeciesList	scientific name: Phytophthora infestans; NCBI TaxID: 4787;
ModificationList	No PTMs are included in the dataset
Instrument	instrument model: LTQ Orbitrap XL; LTQ Orbitrap XL

Revision	Datetime	Status	ChangeLog Entry
0	2013-08-29 00:16:59	ID requested
1	2014-03-27 03:01:25	announced
⏵ 2	2014-07-28 00:46:00	announced	Updated project metadata.

Resj, ö S, Ali A, Meijer HJ, Seidl MF, Snel B, Sandin M, Levander F, Govers F, Andreasson E, Quantitative label-free phosphoproteomics of six different life stages of the late blight pathogen Phytophthora infestans reveals abundant phosphorylation of members of the CRN effector family. J Proteome Res, 13(4):1848-59(2014) [pubmed]

submitter keyword: phosphoproteome

Svante Resjo
contact affiliation	Plant Protection Biology, Swedish University of Agricultural Sciences
contact email	svante.resjo@slu.se
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000433
     1. Label: PRIDE project
     2. Name: Quantitative phosphoproteomics of Phytophthora infestans life stages