PXD003081

PXD003081 is an original dataset announced via ProteomeXchange.

Title	Proteomic Dataset of the organohalide-respiring bacterium Dehalococcoides mccartyi strain CBDB1 grown on hexachlorobenzene as electron acceptor
Description	The proteome of the anaerobic bacterium Dehalococcoides mccartyi strain CBDB1 from the phylum Chloroflexi was investigated. D. mccartyi strain CBDB1 is a model organism for organohalide respiration where halogenated organic compounds serve as terminal electron acceptors. A wide range of halogenated organic compounds have been shown to be dehalogenated by the strain CBDB1. Therefore, D. mccartyi strain CBDB1 is a promising candidate for bioremediation application. Proteomic analysis of cultures grown with hexachlorobenzene as only electron acceptor resulted in identification of 8,491 distinct peptides which represents 1,023 proteins. A coverage of 70% of the 1,458 annotated proteins for strain CBDB1 was achieved. In addition, a spectral library was created from the annotated spectra. By using proteogenomics, 18 previously not annotated peptides were identified which contribute to four proteins previously not annotated and corrections in length of eight protein coding sequences.
HostingRepository	PRIDE
AnnounceDate	2016-03-11
AnnouncementXML	Submission_2016-03-11_07:56:07.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christian Schiffmann
SpeciesList	scientific name: Dehalococcoides mccartyi (strain CBDB1); NCBI TaxID: 255470;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-10-19 23:52:20	ID requested
⏵ 1	2016-03-11 07:56:08	announced

Schiffmann CL, Otto W, Hansen R, Nielsen PH, Adrian L, Seifert J, von Bergen M, Jehmlich N, Proteomic dataset of the organohalide-respiring bacterium Dehalococcoides mccartyi strain CBDB1 grown on hexachlorobenzene as electron acceptor. Data Brief, 7():253-6(2016) [pubmed]

curator keyword: Biological

submitter keyword: Dehalococcoides mccartyi strain CBDB1, organohalide respiration,

Martin von Bergen
contact affiliation	Department of Proteomics, Helmholtz Centre for Environmental Research – UFZ, Permoserstr. 15, 04318 Leipzig, Germany
contact email	martin.vonbergen@ufz.de
lab head
Christian Schiffmann
contact affiliation	Department of Proteomics, Helmholtz Centre for Environmental Research – UFZ, Permoserstr. 15, 04318 Leipzig, Germany
contact email	christian.schiffmann@ufz.de
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/2016/03/PXD003081

PRIDE project URI

• PRIDE
  1. PXD003081
     1. Label: PRIDE project
     2. Name: Proteomic Dataset of the organohalide-respiring bacterium Dehalococcoides mccartyi strain CBDB1 grown on hexachlorobenzene as electron acceptor