PXD000147
PXD000147 is an original dataset announced via ProteomeXchange.
Dataset Summary
Title | Proteomics Analysis of Burkholderia Kirkii |
Description | Protein 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. |
HostingRepository | PRIDE |
AnnounceDate | 2013-09-13 |
AnnouncementXML | Submission_2013-09-13_02:18:51.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Ulrich Omasits |
SpeciesList | scientific name: Candidatus Burkholderia kirkii; NCBI TaxID: 198822; |
ModificationList | L-methionine sulfoxide; deamidated residue; 2-pyrrolidone-5-carboxylic acid (Gln); S-carboxamidomethyl-L-cysteine |
Instrument | LTQ Orbitrap XL |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2013-02-15 03:59:17 | ID requested | |
1 | 2013-07-18 09:10:51 | announced | |
1 | 2014-07-25 00:53:10 | announced | |
⏵ 2 | 2013-09-13 02:18:51 | announced | Add reference |
⏵ 2 | 2014-08-08 00:30:41 | announced | Updated 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 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/PXD000147 |