Email updates

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

Open Access Research article

A proteogenomic analysis of Shigella flexneri using 2D LC-MALDI TOF/TOF

Lina Zhao12, Liguo Liu1, Wenchuan Leng1, Candong Wei1* and Qi Jin1*

Author Affiliations

1 State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China

2 Department of Biological Engineering, College of Life Sciences, Hebei United University, Tangshan City, Hebei Province, P.R. China

For all author emails, please log on.

BMC Genomics 2011, 12:528  doi:10.1186/1471-2164-12-528

Published: 28 October 2011

Additional files

Additional file 1:

Supplementary Table S1, All proteins identified by MS analysis. This file contains detailed information of all identified proteins in our study.

Format: XLS Size: 692KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Supplementary Figures. This file contains supplementary Figures S1-6. Figure S1 illustrates the patterns of pI, Mr, and GRAVY value of identified/annotated proteins. Figure S2 illustrates COGs functional categories of identified/annotated proteins. Figure S3 shows the information about N-terminal extension of three genes. Figure S4 shows RT-PCR results of three extended genes. Figure S5 shows RT-PCR results for BIO11778. Figure S6 illustrates patterns for relative location of novel ORFs overlapping known genes.

Format: DOC Size: 212KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 3:

Supplementary Table S2, List of candidate N-terminal extension genes. This file contains a list of genes that are likely to be extended at the N-terminus in the S. flexneri 2a str.301 genome. Each entry's information includes locus tag, extension region: genome position of region from N-terminal new start codon to the 33rd amino acid residue downstream of original start site for each extended gene, and the peptide sequence corresponding to extension region.

Format: XLS Size: 233KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Manually validated MS/MS spectra. This file shows all MS/MS spectra of peptides matching to annotated proteins that had a single peptide hit (ion score < 45) and un-annotated novel proteins.

Format: DOC Size: 651KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 5:

Supplementary Table S3. Table S3 shows a list of primers used in this article.

Format: DOC Size: 45KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data