Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Highly Accessed Research article

High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade

Joseph A Christie-Oleza, Guylaine Miotello and Jean Armengaud*

Author Affiliations

CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France

For all author emails, please log on.

BMC Genomics 2012, 13:73  doi:10.1186/1471-2164-13-73

Published: 15 February 2012

Additional files

Additional file 1:

Non-redundant peptide list detected by MS/MS spectral attributions (p < 0.005). The excel table presents the characteristics of all the non-redundant peptides detected (22805 items) and their corresponding proteins.

Format: XLS Size: 6.8MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Stop-to-stop polypeptides detected by MS/MS. The excel table presents the whole list (2547 items) of ORFs detected by MS/MS with their annotated function and sequence, as well as the number of non-redundant peptides assigned to each of these ORFs.

Format: XLS Size: 1.4MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

List of novel genes encoded in the genome of R. pomeroyi detected by proteogenomics in this study. The excel table presents the 39 new genes found in the present study and their characteristics. The corresponding ORF, the number of non-redundant peptides, the number of MS/MS spectra assigned, the plausible protein sequence, and the conditions where each product has been detected are listed for the 39 genes.

Format: XLS Size: 144KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Annotated CDS demonstrated to be longer due to the detection of tryptic peptides situated further N-ter than previously annotated. The excel table presents the evidences for 10 annotated CDS that should be revised in terms of N-terminus. The corresponding ORF label, the number of non-redundant peptides, the new proteomic-corrected CDS sequence and the corresponding peptide evidences (peptide query, peptide sequence, peptide score) are indicated for each of these 10 CDS.

Format: XLS Size: 38KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

Semi-tryptic peptides representing the most N-ter sequence of the stop-to-stop CDS. The excel table presents the characteristics of all the semi-tryptic peptides detected which correspond to the most N-terminal sequence of the stop-to-stop ORF (22805 items) and their corresponding proteins. We distinguished the peptides starting with a methionine residue encoded by an ATG start codon (lines 5-136), those starting from the residue just after a removed methionine encoded by an ATG start codon (lines 138-463), the peptides starting with a methionine residue encoded by an GTG start codon (lines 465-471), those starting from the residue just after a removed methionine encoded by an GTG start codon (lines 473-489), and those starting from the residue just after a removed methionine encoded by an TTG start codon (lines 491-494).

Format: XLS Size: 601KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

Ortho-proteogenomic based analysis extending the N-ter corrections done on R. pomeroyi to 36 other isolates of the Roseobacter clade. The excel table presents the extension to 36 isolates for each of R. pomeroyi re-annotated genes (9887 proposals). The e-value obtained by BLAST is indicated for each homologue, as well as its N-terminus (60 first residues), the new CDS length, and its location on the corresponding genome.

Format: XLS Size: 3.5MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Primers used throughout the study for PCR amplifications. The excel table presents the 37 primers used in the study for PCR amplification of specific genomic loci and their characteristics (sequence, position, names, melting temperature, targets).

Format: XLS Size: 40KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data