PXD000270-3

PXD000270 is an original dataset announced via ProteomeXchange.

Title	Proteome of Burkholderia cenocepacia H111 in aerobic and micro-oxia condition
Description	Using a discovery shotgun proteomics approach, the expressed proteome of Burkholderia cenocepacia (strain H111) under aerobic (21% oxygen) and micro-oxic (0.5% oxygen) conditions was analyzed. B.cenocepacia is an opportunistic human pathogen that is particularly problematic for patients suffering from cystic fibrosis. Cells were sub-cellular fractionated (Cyt=cytoplasmic, TM=total membrane, EC=extracellular) and proteins were extracted and separated by 1D SDS-PAGE. Gels were cut into ten slices, digested using trypsin and resulting peptides were analyzed using LC-MS/MS once with a discovery run followed by a subsequent exclusion list run (precursor ions identified in the discovery run were excluded from fragmentation in the exclusion run). Mass spectra were searched against a protein sequence database containing 7258 annotated B. cenocepacia H111 proteins (accession CAFQ00000000.1) and protein sequences of 259 common contaminants. Spectra were searched against this database with MS-GF+ (MS-GFDB v7747, kindly provided by Dr. Sangtae Kim, UCSD, USA) using the following parameters: Carbamidomethylation was set as a fixed modification on all Cysteines, oxidation of Methionines, deamidation of Asparagines and Glutamines, as well as cyclization of N-terminal Glutamines were considered as optional modifications. Spectra were searched for a match to fully-tryptic and semi-tryptic peptides and the automatic decoy search option was enabled. Search results were filtered and summarized using in-house tools. A total of 2,128 proteins was identified at an estimated FDR of less than 1%. Additional RNA-seq data are held at GEO under the accession: GSE48585.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:17:09.769.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ulrich Goldmann
SpeciesList	scientific name: Burkholderia cenocepacia H111; NCBI TaxID: 1055524;
ModificationList	(R)-5-oxo-1; monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-05-30 03:10:58	ID requested
1	2013-07-18 07:37:26	announced
1	2014-07-25 01:13:21	announced
2	2013-09-12 02:56:35	announced	Add reference
⏵ 3	2024-10-22 04:17:10	announced	2024-10-22: Updated project metadata.

Pessi G, Braunwalder R, Grunau A, Omasits U, Ahrens CH, Eberl L, Response of Burkholderia cenocepacia H111 to micro-oxia. PLoS One, 8(9):e72939(2013) [pubmed]

10.1371/journal.pone.0072939;

submitter keyword: shotgun LC-MS/MS, cystic fibrosis,Burkholderia cepacia complex (Bcc), biofilm

Ulrich Goldmann
contact affiliation	CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences
contact email	ugoldmann@cemm.at
lab head
Ulrich Goldmann
contact affiliation	CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences
contact email	ugoldmann@cemm.at
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/2013/07/PXD000270

PRIDE project URI

• PRIDE
  1. PXD000270
     1. Label: PRIDE project
     2. Name: Proteome of Burkholderia cenocepacia H111 in aerobic and micro-oxia condition