PXD000270
PXD000270 is an original dataset announced via ProteomeXchange.
Dataset Summary
| 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 | 2013-09-12 |
| AnnouncementXML | Submission_2013-09-12_02:56:35.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Ulrich Omasits |
| SpeciesList | scientific name: Burkholderia cenocepacia H111; NCBI TaxID: 1055524; |
| ModificationList | iodoacetamide derivatized residue; deamidated residue; monohydroxylated residue; (R)-5-oxo-1: 4-tetrahydrothiazine-3-carboxylic acid |
| Instrument | LTQ Orbitrap |
Dataset History
| 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 |
Publication List
| 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] |
Keyword List
| submitter keyword: Burkholderia cepacia complex (Bcc), cystic fibrosis, biofilm, shotgun LC-MS/MS |
Contact List
| Ulrich Omasits | |
|---|---|
| contact affiliation | Institute of Molecular Systems Biology, ETH Zurich |
| contact email | omasitsu@ethz.ch |
Full Dataset Link List
| 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/2013/07/PXD000270 |
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