Dataset Information

Improving Genome Annotation of Enterotoxigenic Escherichia coli TW10598 by a Label-Free Quantitative MS/MS Approach

ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Escherichia Coli

SUBMITTER: Veronika Kucharova

LAB HEAD: Harald G. Wiker

PROVIDER: PXD002473 | Pride | 2015-09-15

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	14-11-12TW105984BioRepagainstTW105986-frametranslation.zip	Other
	14-11-12TW105984BioRepagainstUniProt.zip	Other
	14-11-13TW105984BioRepagainstUniProt.zip	Other
	14-11-14TW105984BioRepagainstUniProtandTW105986frame.zip	Other
	14-11-17TW105984BioRepagainstTW105986-frametranslation.zip	Other

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Publications

Improving genome annotation of enterotoxigenic Escherichia coli TW10598 by a label-free quantitative MS/MS approach.

Pettersen Veronika Kuchařová VK Steinsland Hans H Wiker Harald G HG

Proteomics 20151007 22

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. Here, we report a synonymous proteogenomic approach for experimentally improving microbial genome annotation based on label-free quantitative MS/MS. The approach is exemplified by analysis of cell extracts from in vitro cultured enterotoxigenic Escherichia col ...[more]

PMID: 26349841

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