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PXD000337-2

PXD000337 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleN-terminal-oriented proteogenomics for the marine bacterium Roseobacter denitrificans
DescriptionGiven 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.
HostingRepositoryPRIDE
AnnounceDate2014-07-25
AnnouncementXMLSubmission_2014-07-25_01:21:59.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterJean ARMENGAUD
SpeciesList scientific name: Roseobacter denitrificans (strain ATCC 33942 / OCh 114) (Erythrobacter sp. (strain OCh 114)) (Roseobacter denitrificans); NCBI TaxID: 375451;
ModificationListmonohydroxylated residue; acetylated residue
InstrumentLTQ Orbitrap
Dataset History
RevisionDatetimeStatusChangeLog Entry
02013-07-11 05:45:10ID requested
12014-02-19 05:46:01announced
22014-07-25 01:22:00announcedUpdated project metadata.
Publication List
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]
Keyword List
submitter keyword: proteogenomics, genome annotation, N-terminomics, high-throughput proteomics, protein derivatization, tandem mass spectrometry
Contact List
Jean ARMENGAUD
contact affiliationSBTN
contact emailjean.armengaud@cea.fr
dataset submitter
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Dataset FTP location
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