Proteome of Burkholderia cenocepacia H111 in aerobic and micro-oxia condition

ABSTRACT: Using a discovery shotgun proteomics approach, the expressed proteome of Burkholderia cenocepacia (strain H111) under aerobic (21% oxygen) and micro-oxic (0.5% oxygen) conditions was analyzed. B.cenocepacia is an opportunistic human pathogen that is particularly problematic for patients suffering from cystic fibrosis. Cells were sub-cellular fractionated (Cyt=cytoplasmic, TM=total membrane, EC=extracellular) and proteins were extracted and separated by 1D SDS-PAGE. Gels were cut into ten slices, digested using trypsin and resulting peptides were analyzed using LC-MS/MS once with a discovery run followed by a subsequent exclusion list run (precursor ions identified in the discovery run were excluded from fragmentation in the exclusion run). Mass spectra were searched against a protein sequence database containing 7258 annotated B. cenocepacia H111 proteins (accession CAFQ00000000.1) and protein sequences of 259 common contaminants. Spectra were searched against this database with MS-GF+ (MS-GFDB v7747, kindly provided by Dr. Sangtae Kim, UCSD, USA) using the following 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. Spectra were searched for a match to fully-tryptic and semi-tryptic peptides and the automatic decoy search option was enabled. Search results were filtered and summarized using in-house tools. A total of 2,128 proteins was identified at an estimated FDR of less than 1%. Additional RNA-seq data are held at GEO under the accession: GSE48585.

OTHER RELATED OMICS DATASETS IN: PRJNA210753

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Burkholderia Cenocepacia H111

SUBMITTER: Ulrich Goldmann  

PROVIDER: PXD000270 | Pride | 2013-07-18

REPOSITORIES: Pride