PXD000221

PXD000221 is an original dataset announced via ProteomeXchange.

Title	Proteins from Outer Membrane Vesicules of Pseudomonas syringae Lz4W
Description	The proteins from Outer Membrane Vesicles (OMVs) were extracted by chilled acetone method. The proteins were separated on 1D SDS-PAGE (12%). From the gel, total 10 fractions were made and all of them were subjected to in gel digestion using trypsin. The MS/MS spectra of the resulting tryptic peptides were recordedby using LC coupled ESI-MS/MS (Thermo Orbitrap Velos). The mass spectral data thus obtained was analysed by using Proteome Discoverer 1.3. Since the genome sequence of P. syringae Lz4W is not available, the data was searched against a database prepared from 20 related Pseudomonas species whose genome sequence is available on Uniprot (Updated upto Jan 2013). The search was observed by using nodes Sequest and Mascot both, the enzyme selected was trypsin with maximum 2 missed cleavages, the precursor tolerance set at 10 ppm, fragment tolerance at 0.8 Da, carbamidomethylated cystein (57.02 Da) as fixed modification, oxidised methionine (15.99 Da) as variable modification. After the search is over, the results were refined applying result filters as Peptide confidence (High) and Differentiable Proteins (including distinct proteins), which makes sure that each protein entry in the list is identified with at least one unique peptide.
HostingRepository	PRIDE
AnnounceDate	2014-07-25
AnnouncementXML	Submission_2014-07-25_01:04:22.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jagannadham Medicharla V
SpeciesList	scientific name: Pseudomonas sp.; NCBI TaxID: 306;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2013-04-23 02:05:16	ID requested
1	2014-01-29 07:19:25	announced
⏵ 2	2014-07-25 01:04:23	announced	Updated project metadata.

Kulkarni HM, Swamy ChV, Jagannadham MV, Molecular characterization and functional analysis of outer membrane vesicles from the antarctic bacterium Pseudomonas syringae suggest a possible response to environmental conditions. J Proteome Res, 13(3):1345-58(2014) [pubmed]

submitter keyword: outer membrane vesicles, antarctic bacteria

Jagannadham Medicharla V
contact affiliation	Center for Cellular and Molecular Biology
contact email	jagan@ccmb.res.in
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/2014/01/PXD000221

PRIDE project URI

• PRIDE
  1. PXD000221
     1. Label: PRIDE project
     2. Name: Proteins from Outer Membrane Vesicules of Pseudomonas syringae Lz4W