PXD018338

PXD018338 is an original dataset announced via ProteomeXchange.

Title	SWATH-based quantitative proteomics data derived from whole grain of Malaysian local pigmented and non-pigmented rice varieties
Description	Information about protein expression in rice grain across both pigmented and non-pigmented rice varieties is still relatively scarce. The data provided here represent proteomic data obtained from selected 6 Malaysian local rice varieties with varying pigmentations (black, red and white). The selected pigmented rice varieties such as black (BALI and Pulut hitam 9) and red rice (MRQ100 and MRM16) have shown high antioxidant activities and non-pigmented rice (MRQ76 and MR297) contain amino acid and micronutrient contents. This project aimed to obtain global protein expression profile as well as differential protein expression between the selected pigmented and non-pigmented rice varieties particularly proteins with their functions responsible for nutritional (i.e. antioxidant, folate and low glycaemic index) and quality (i.e. aromatic) traits. Integration of this proteomics dataset with other available in-house omics data could facilitate the identification of significant functional markers related to nutritional and quality traits. Total proteins were prepared from dehusked matured seeds harvested from three different rice plants of each variety (3 protein samples per variety). The proteins were trypsin digested before subjected to SWATH-MS proteomics analysis. Proteins were identified by matching tandem mass (MS/MS) spectra from both 1D and 2D IDA to Oryza sativa japonica and indica rice databases available at UniProt by using ProteinPilot software (v4.2) (AB Sciex). Quantification of proteins was carried out by determining protein peak areas extracted from SWATH analysis data sets using PeakView (v2.1) (AB Sciex) software. Differentially expressed protein between varieties were identified using T-test analysis with a set threshold for fold change ± 1.5 and p‐value < 0.05.
HostingRepository	PRIDE
AnnounceDate	2020-04-27
AnnouncementXML	Submission_2020-04-26_23:35:21.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Wan Aizat
SpeciesList	scientific name: Oryza sativa (Rice); NCBI TaxID: 4530;
ModificationList	iodoacetamide derivatized residue
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2020-04-02 06:01:24	ID requested
⏵ 1	2020-04-26 23:35:21	announced

Dataset with its publication pending

submitter keyword: Oryza sativa indica

pigmented rice

non-pigmented rice

nutritional traits

SWATH-MS.

Dr. Norliza Abu Bakar
contact affiliation	Principal Research Officer Malaysian Agricultural Research & Development Institute (MARDI), 43300 Serdang, Selangor, Malaysia
contact email	lizaab@mardi.gov.my
lab head
Wan Aizat
contact affiliation	Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor, Malaysia
contact email	wma@ukm.edu.my
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/2020/04/PXD018338

PRIDE project URI

• PRIDE
  1. PXD018338
     1. Label: PRIDE project
     2. Name: SWATH-based quantitative proteomics data derived from whole grain of Malaysian local pigmented and non-pigmented rice varieties