PXD000337-2

PXD000337 is an original dataset announced via ProteomeXchange.

Title	N-terminal-oriented proteogenomics for the marine bacterium Roseobacter denitrificans
Description	Given the facilities for whole genome sequencing with next-generation sequencers, structural and functional gene annotation is now only based on automated prediction. However, errors in terms of gene structure are still frequently reported especially for the correct determination of initiation start codons. Here, we propose a strategy to enrich and detect protein N-termini by mass spectrometry in order to refine genome annotation. After selective protein N-termini derivatization using (N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPPAc-OSu) as labeling reagent, protein digestion was performed with three proteases in parallel. TMPP-labeled N-terminal-most peptides were further resolved from internal peptides by the COmbined FRActional DIagonal Chromatography (COFRADIC) sorting methodology before analysis with tandem mass spectrometry. We refined the annotation of the genome of a model marine bacterium, Roseobacter denitrificans.
HostingRepository	PRIDE
AnnounceDate	2014-07-25
AnnouncementXML	Submission_2014-07-25_01:21:59.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jean ARMENGAUD
SpeciesList	scientific name: Roseobacter denitrificans (strain ATCC 33942 / OCh 114) (Erythrobacter sp. (strain OCh 114)) (Roseobacter denitrificans); NCBI TaxID: 375451;
ModificationList	monohydroxylated residue; acetylated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-07-11 05:45:10	ID requested
1	2014-02-19 05:46:01	announced
⏵ 2	2014-07-25 01:22:00	announced	Updated project metadata.

Bland C, Hartmann EM, Christie-Oleza JA, Fernandez B, Armengaud J, N-Terminal-oriented proteogenomics of the marine bacterium roseobacter denitrificans Och114 using N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) labeling and diagonal chromatography. Mol Cell Proteomics, 13(5):1369-81(2014) [pubmed]

submitter keyword: proteogenomics, genome annotation, N-terminomics, high-throughput proteomics, protein derivatization, tandem mass spectrometry

Jean ARMENGAUD
contact affiliation	SBTN
contact email	jean.armengaud@cea.fr
dataset submitter

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/2014/02/PXD000337

PRIDE project URI

• PRIDE
  1. PXD000337
     1. Label: PRIDE project
     2. Name: N-terminal-oriented proteogenomics for the marine bacterium Roseobacter denitrificans