<<< Full experiment listing

PXD002473

PXD002473 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleImproving Genome Annotation of Enterotoxigenic Escherichia coli TW10598 by a Label-Free Quantitative MS/MS Approach
DescriptionThe 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.
HostingRepositoryPRIDE
AnnounceDate2015-09-15
AnnouncementXMLSubmission_2015-09-15_06:32:57.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterVeronika Kucharova
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationListNo PTMs are included in the dataset
InstrumentLTQ Orbitrap Velos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02015-07-03 06:12:16ID requested
12015-09-15 06:32:58announced
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 affiliationThe Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, Norway
contact emailHarald.Wiker@uib.no
lab head
Veronika Kucharova
contact affiliationUniversity of Bergen
contact emailveronika.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
[ + ]