PXD005586-2

PXD005586 is an original dataset announced via ProteomeXchange.

Title	Characterization of the proteome of Theobroma cacao beans by nanoUHPLC-ESI MS/MS
Description	Cocoa seed storage proteins play an important role in flavour development as aroma precursors are formed from their degradation during fermentation. Major proteins in the beans of Theobroma cacao are the storage proteins belonging to the vicilin and albumin fraction. Although both these classes of proteins have been fully characterized, there is still limited information on the expression and abundance of other proteins present in cocoa beans. This work is the first attempt to characterize the whole cocoa bean proteome by nanoUHPLC-ESI MS/MS analysis using tryptic digests of cocoa bean protein extracts. The results of this analysis show that a total of 906 proteins could be identified using a species-specific Theobroma cacao database. The majority of the identified proteins were involved with metabolism and energy. However, a significant number of the identified proteins were linked to protein synthesis and processing. Several proteins were also involved with plant response to stress conditions and defence. Albumin and vicilin storage proteins showed the highest intensity values among all detected proteins, although only seven entries were identified as storage proteins. A comparison of MS/MS data searches carried out against larger non-specific databases confirmed that using a species-specific database can increase the number of identified proteins, and at the same time reduce the number of false positives. The results of this work will be useful in developing tools which can allow the comparison of the proteomic profile of cocoa beans from different genotypes and geographic origins.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:35:08.354.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Emanuele Scollo
SpeciesList	scientific name: Theobroma cacao (Cacao) (Cocoa); NCBI TaxID: 3641;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2016-12-16 03:54:16	ID requested
1	2018-01-04 02:35:52	announced
⏵ 2	2024-10-22 04:35:11	announced	2024-10-22: Updated project metadata.

Scollo E, Neville D, Oruna-Concha MJ, Trotin M, Cramer R, Characterization of the Proteome of Theobroma cacao Beans by Nano-UHPLC-ESI MS/MS. Proteomics, 18(3-4):(2018) [pubmed]

10.1002/pmic.201700339;

curator keyword: Biological

submitter keyword: plant proteomics, storage proteins, cocoa bean proteome,Theobroma cacao, cocoa beans

Prof Rainer Cramer
contact affiliation	Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
contact email	r.k.cramer@reading.ac.uk
lab head
Emanuele Scollo
contact affiliation	University of Reading
contact email	e.scollo@hotmail.it
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/2018/01/PXD005586

PRIDE project URI

• PRIDE
  1. PXD005586
     1. Label: PRIDE project
     2. Name: Characterization of the proteome of Theobroma cacao beans by nanoUHPLC-ESI MS/MS