PXD011984

PXD011984 is an original dataset announced via ProteomeXchange.

Title	UHPLC-MS/MS analysis of the proteomic profiles of cocoa beans from different genotypes
Description	Amongst other compounds, cocoa flavour is dependent on peptides that are formed during fermentation of cocoa beans from proteins such as albumin and vicilin. In this study the proteomic profiles of cocoa beans from four genotypes (ICS 1, ICS 39, IMC 67 and SCA 6) with different genetic background and flavour profiles have been analysed by employing a bottom-up label free LC-MS/MS approach. From a total of 430 identified proteins, 250 proteins were found significantly differentially expressed among the four cocoa genotypes analysed. Of these, 61 proteins with a fold change of 2 or more were further investigated, showing that the majority is involved in stress response. Furthermore, several of these 61 proteins could also be linked to oxidation-reduction processes. PCA analysis allowed a clear separation of the genotypes based on their proteomic profile, with an aminohydrolase and a sulphite oxidase greatly contributing to the separation. Aspartyl protease was more abundant in the genotypes ICS 1 and ICS compared to IMC 67, while a serine carboxypeptidase was significantly more expressed in the genotype ICS 39 in comparison with the other genotypes. Both these enzymes catalyse the degradation of storage proteins during fermentation. A Beta-amylase, an enzyme which catalyses the release of maltose was detected at a significantly higher level in the genotype SCA 6 compared to ICS 1 and IMC 67. Two Amine oxidases were significantly more abundant in the genotype SCA 6 compared to ICS 39, and in the genotype ICS 1 versus ICS 39, while two alcohol dehydrogenase were higher expressed in the genotype SCA 6 compared to IMC 67. These enzyme catalyse oxidation of amines and alcohols with release of aldehydes and ketones. The data shows that UHPLC-MS/MS can be employed to differentiate cocoa beans from various varieties, and thus in theory be linked to differences in their flavour profile.
HostingRepository	PRIDE
AnnounceDate	2019-08-15
AnnouncementXML	Submission_2019-08-30_00:43:55.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD011984
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Emanuele Scollo
SpeciesList	scientific name: Theobroma cacao (Cacao) (Cocoa); NCBI TaxID: 3641;
ModificationList	Oxidation; Acetyl; Carbamidomethyl
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-12-10 01:42:37	ID requested
1	2019-08-15 02:56:14	announced
⏵ 2	2019-08-30 00:43:56	announced	Updated publication reference for PubMed record(s): 31445177.

Scollo E, Neville DCA, Oruna-Concha MJ, Trotin M, Cramer R, UHPLC-MS/MS analysis of cocoa bean proteomes from four different genotypes. Food Chem, 303():125244(2020) [pubmed]

curator keyword: Biological

submitter keyword: Cocoa beans, label free quantitation, plant proteomics, cocoa beans proteome, Theobroma cacao

Professor Rainer Cramer
contact affiliation	University of Reading
contact email	r.k.cramer@rdg.ac.uk
lab head
Emanuele Scollo
contact affiliation	University of Reading
contact email	e.scollo@hotmail.it
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD011984
     1. Label: PRIDE project
     2. Name: UHPLC-MS/MS analysis of the proteomic profiles of cocoa beans from different genotypes