PXD002473 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Improving Genome Annotation of Enterotoxigenic Escherichia coli TW10598 by a Label-Free Quantitative MS/MS Approach |
Description | The most commonly used genome annotation processes are to a great extent based on computational methods. However, those can only predict genes that have been described earlier or that have sequence signatures indicative of a gene function. We reported a synonymous proteogenomic approach for experimentally improving microbial genome annotation based on label-free quantitative MS/MS. The approach was exemplified by analysis of cell extracts from in vitro cultured enterotoxigenic Escherichia coli (ETEC) strain TW10598, as part of an effort to create a new reference ETEC genome sequence. The proteomic analysis yielded identification of 2,060 proteins, out of which 274 proteins were originally described as hypothetical. For 84% of the identified proteins we have provided description of their relative quantitative levels, among others, for 20 abundantly expressed ETEC virulence factors. Proteogenomic mapping supported the existence of four protein-coding genes that had not been annotated, and led to correction of translation start positions of another nine. |
HostingRepository | PRIDE |
AnnounceDate | 2015-09-15 |
AnnouncementXML | Submission_2015-09-15_06:32:57.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Veronika Kucharova |
SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; |
ModificationList | No PTMs are included in the dataset |
Instrument | LTQ Orbitrap Velos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2015-07-03 06:12:16 | ID requested | |
⏵ 1 | 2015-09-15 06:32:58 | announced | |
Publication List
Pettersen VK, Steinsland H, Wiker HG, Improving genome annotation of enterotoxigenic Escherichia coli TW10598 by a label-free quantitative MS/MS approach. Proteomics, 15(22):3826-34(2015) [pubmed] |
Keyword List
curator keyword: Biological, Technical |
submitter keyword: Genome Annotation, Enterotoxigenic Escherichia coli, Synonymous Proteogenomics, Label-Free Quantification |
Contact List
Harald G. Wiker |
contact affiliation | The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, Norway |
contact email | Harald.Wiker@uib.no |
lab head | |
Veronika Kucharova |
contact affiliation | University of Bergen |
contact email | veronika.kucharova@k2.uib.no |
dataset submitter | |
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/pride/data/archive/2015/09/PXD002473 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD002473
- Label: PRIDE project
- Name: Improving Genome Annotation of Enterotoxigenic Escherichia coli TW10598 by a Label-Free Quantitative MS/MS Approach