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PXD000147

PXD000147 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleProteomics Analysis of Burkholderia Kirkii
DescriptionProtein extract from symbiontic Burkholderia Kirkii (3 replicates: A,B,C): each fractionated by SDS-PAGE and digested using Trypsin, each fraction measured twice in LC-MSMS, once in discovery mode and once using an exclusion list based on first run. Mass spectra were searched against a protein sequence database containing products of both predicted protein coding genes and pseudogenes for B. kirkii, genes predicted by the Prodigal software, genes predicted by in-house software, P. kirkii chloroplastic proteins, as well as protein sequences of 256 common contaminants. We used Mascot search engine (version 2.3.0) with the following search 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. Precursor ion mass tolerance was set to 10 ppm, fragment ion mass tolerance was set to 0.8 Da, and the automatic decoy search option was enabled. Spectra were searched for a match to fully-tryptic and semi-tryptic peptides with up to two missed cleavage sites. The built-in version of Mascot Percolator was used to improve the peptide spectrum match (PSM) scores. Peptides were assessed with the PeptideClassifier software. Additional genome annotation is held at ENA under the accession: WGS project CAFE00000000.
HostingRepositoryPRIDE
AnnounceDate2013-09-13
AnnouncementXMLSubmission_2013-09-13_02:18:51.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterUlrich Omasits
SpeciesList scientific name: Candidatus Burkholderia kirkii; NCBI TaxID: 198822;
ModificationListL-methionine sulfoxide; deamidated residue; 2-pyrrolidone-5-carboxylic acid (Gln); S-carboxamidomethyl-L-cysteine
InstrumentLTQ Orbitrap XL
Dataset History
RevisionDatetimeStatusChangeLog Entry
02013-02-15 03:59:17ID requested
12013-07-18 09:10:51announced
12014-07-25 00:53:10announced
22013-09-13 02:18:51announcedAdd reference
22014-08-08 00:30:41announcedUpdated project metadata.
Publication List
Carlier AL, Omasits U, Ahrens CH, Eberl L, Proteomics analysis of Psychotria leaf nodule symbiosis: improved genome annotation and metabolic predictions. Mol Plant Microbe Interact, 26(11):1325-33(2013) [pubmed]
Keyword List
submitter keyword: Burkholderia Kirkii
Contact List
Ulrich Omasits
contact affiliationInstitute of Molecular Systems Biology, ETH Zurich
contact emailomasitsu@ethz.ch
Full Dataset Link List
Dataset FTP location
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