PXD000403

PXD000403 is an original dataset announced via ProteomeXchange.

Title	Sphingomonas wittichii RW1 shotgun proteomics
Description	Chlorinated congeners of dibenzo-p-dioxin and dibenzofuran are widely dispersed pollutants that can be treated using microorganisms, such as the Sphingomonas wittichii RW1 bacterium, able to transform some of them into non-toxic substances. The enzymes of the upper pathway for dibenzo-p-dioxin degradation in S. wittichii RW1 have been biochemically and genetically characterized, but its genome sequence has indicated the existence of a tremendous potential for aromatic compound transformation, with 56 ring-hydroxylating dioxygenase subunits, 34 extradiol dioxygenases, and 40 hydrolases. To further characterize this enzymatic arsenal, new methodological approaches should be employed. Here, a large shotgun proteomic survey has been performed on cells grown on dibenzofuran, dibenzo-p-dioxin, and 2-chlorodibenzo-p-dioxin, and compared to growth on acetate. Changes in the proteome were monitored over time. Peak lists were generated with the Mascot Daemon software (version 2.3.2; Matrix Science, London, UK) using the extract_msn.exe data import filter (Thermo Fisher Scientific) from the Xcalibur FT package (version 2.0.7; Thermo Fisher Scientific). Data import filter options were set to 400 (minimum mass), 5000 (maximum mass), 0 (grouping tolerance), 0 (intermediate scans) and 1000 (threshold). The mgf files from technical triplicates were merged, and MS/MS spectra were assigned using the Mascot Daemon 2.3.2 (Matrix Science) and a database containing the nonredundant RefSeq protein entries for S. wittichii RW1 (NCBI Taxonomy ID: 392499), comprising 5345 protein sequences totalling 1 800 684 amino acids. The search was performed using the following criteria: tryptic peptides with a maximum of two miscleavages, mass tolerances of 5 ppm on the parent ion and 0.5 Da on the MS/MS, fixed modification for carbamidomethylated cysteine, and variable modification for methionine oxidation. Mascot results were parsed using the IRMa 1.28.0 software. Peptides were identified with a P-value threshold below 0.05. Proteins were considered validated when at least two distinct peptides were detected. Using a selection of 11 result files and the appropriate decoy database, the false discovery rate for protein identification was estimated to be 0.33% with these parameters.
HostingRepository	PRIDE
AnnounceDate	2014-08-08
AnnouncementXML	Submission_2014-08-08_01:54:50.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000403
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Jean ARMENGAUD
SpeciesList	scientific name: Sphingomonas wittichii; NCBI TaxID: 160791;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap; instrument model: LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-08-06 03:17:49	ID requested
1	2013-10-22 05:43:07	announced
1	2013-10-22 08:25:46	announced
2	2014-07-28 00:44:03	announced	Updated project metadata.
⏵ 3	2014-08-08 01:54:51	announced	Updated project metadata.

Hartmann EM, Armengaud J, Shotgun proteomics suggests involvement of additional enzymes in dioxin degradation by Sphingomonas wittichii RW1. Environ Microbiol, 16(1):162-76(2014) [pubmed]

curator keyword: Biological

submitter keyword: sphingomonas wittichii RW1 dioxin dibenzofuran

Jean ARMENGAUD
contact affiliation	SBTN
contact email	jean.armengaud@cea.fr
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000403
     1. Label: PRIDE project
     2. Name: Sphingomonas wittichii RW1 shotgun proteomics