PXD004896

PXD004896 is an original dataset announced via ProteomeXchange.

Title	N-terminomics Proteogenomics
Description	Proteogenomics is a research field where proteome data is used to improve gene annotation. To achieve this, customized protein databases are constructed to match proteomic data. We perform a proteogenomic analysis using N-terminal COFRADIC data in order to identify novel translational initiation start sites. We use a multistage search strategy where spectra that remained unidentified after searching the Arabidopsis proteome are used for our proteogenomic analysis. Here, the unidentified spectra were searched against a customized N-terminal peptide library derived from a six-frame translation of the Arabidopsis (Arabidopsis thaliana) genome as well as Augustus predicted gene models.
HostingRepository	PRIDE
AnnounceDate	2017-04-26
AnnouncementXML	Submission_2017-04-26_04:21:16.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD004896
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Patrick Willems
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	Oxidation; Acetyl; Carbamidomethyl; Gln->pyro-Glu
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2016-08-25 02:56:35	ID requested
⏵ 1	2017-04-26 04:21:17	announced

Willems P, Ndah E, Jonckheere V, Stael S, Sticker A, Martens L, Van Breusegem F, Gevaert K, Van Damme P, N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana. Mol Cell Proteomics, 16(6):1064-1080(2017) [pubmed]

submitter keyword: N-terminal COFRADIC, Arabidopsis thaliana, positional proteomics, proteogenomics, ribosome profiling, ribo-seq

Petra Van Damme
contact affiliation	Medical Biotechnology Center, VIB, 9000 Ghent, Belgium and Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
contact email	Petra.VanDamme@vib-ugent.be
lab head
Patrick Willems
contact affiliation	PSB-VIB
contact email	pawil@psb.ugent.be
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/2017/04/PXD004896

PRIDE project URI

• PRIDE
  1. PXD004896
     1. Label: PRIDE project
     2. Name: N-terminomics Proteogenomics