PXD045998

PXD045998 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Proteogenomics Pipeline For Pineapple
Description	Here we have undertaken a pilot study analysing the proteome of MD2 pineapple using Liquid Chromatography coupled with Mass Spectrometry (LC-MS/MS) and identified 3,818 peptides from 1,781 candidate proteins in the annotated V3 genome sequenced. In addition, a further 603 peptide identifications were found that mapped exclusively to an independent MD2 transcriptome-derived database and were not found in the standard V3 annotated proteome. Peptide identifications derived from the MD2 transcripts were also cross-referenced to a more recent and complete MD2 genome annotation, resulting in 402 non overlapping peptides with either of the genomes. Subsequently, cross-referencing these peptide identifications via their parent transcripts, 30 high-quality gene candidates novel to the V3 pineapple genomes were identified. These analyses add to the knowledge of experimentally validated pineapple genes and demonstrate the utility of transcript-derived proteomics to discover both novel genes and genetic structure in plant genome, and can help improve its annotation.
HostingRepository	PRIDE
AnnounceDate	2024-05-24
AnnouncementXML	Submission_2024-05-24_02:52:53.887.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	David Newman
SpeciesList	scientific name: Ananas comosus; NCBI TaxID: 4615;
ModificationList	monohydroxylated residue
Instrument	LTQ Orbitrap Elite

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-09 08:47:37	ID requested
⏵ 1	2024-05-24 02:52:54	announced

Publication List

10.1021/acs.jproteome.3c00675;
Ariffin N, Newman DW, Nelson MG, O'cualain R, Hubbard SJ, Proteogenomic Gene Structure Validation in the Pineapple Genome. J Proteome Res, 23(5):1583-1592(2024) [pubmed]

10.1021/acs.jproteome.3c00675;

Ariffin N, Newman DW, Nelson MG, O'cualain R, Hubbard SJ, Proteogenomic Gene Structure Validation in the Pineapple Genome. J Proteome Res, 23(5):1583-1592(2024) [pubmed]

Keyword List

submitter keyword: Orbitrap Elite, MaxQuant,Pineapple, LC-MS/MS

submitter keyword: Orbitrap Elite, MaxQuant,Pineapple, LC-MS/MS

Contact List

Simon Hubbard
contact affiliation	Vice-Dean and Head of School, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
contact email	simon.hubbard@manchester.ac.uk
lab head
David Newman
contact affiliation	University of Oxford
contact email	david.newman@ndm.ox.ac.uk
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/2024/05/PXD045998
PRIDE project URI

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/2024/05/PXD045998

PRIDE project URI

Repository Record List

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