Dataset Information

Proteomics Analysis of Burkholderia Kirkii

ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap XL

ORGANISM(S): Candidatus Burkholderia Kirkii

SUBMITTER: Ulrich Goldmann

PROVIDER: PXD000147 | Pride | 2013-07-18

REPOSITORIES: Pride

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Publications

Proteomics analysis of Psychotria leaf nodule symbiosis: improved genome annotation and metabolic predictions.

Carlier Aurelien L AL Omasits Ulrich U Ahrens Christian H CH Eberl Leo L

Molecular plant-microbe interactions : MPMI 20131101 11

Several plant species of the genus Psychotria (Rubiaceae) harbor Burkholderia sp. bacteria within specialized leaf nodules. The bacteria are transmitted vertically between plant generations and have not yet been cultured outside of their host. This symbiosis is considered to be obligatory because plants devoid of symbionts fail to develop into mature individuals. The genome of 'Candidatus Burkholderia kirkii' has been sequenced recently and has revealed evidence of reductive genome evolution, as ...[more]

PMID: 23902262

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			Action	DRS
	20120305_03_bkirA1.RAW	Raw
	20120305_03_bkirB1.RAW	Raw
	20120305_04_bkirA2.RAW	Raw
	20120305_04_bkirB2.RAW	Raw
	20120305_05_bkirA3.RAW	Raw