PXD005401

PXD005401 is an original dataset announced via ProteomeXchange.

Title	SWATH-MS quantitative analysis of proteins in the rice inferior and superior spikelets during grain filling
Description	Modern rice cultivars have large panicle, however, yield potential of these cultivars is often not fully achieved due to the poor grain-filling of their late-flowering inferior spikelets (IS). Our earlier work suggests broad transcriptional reprogramming during grain filling and shows a difference in gene expression between IS and the earlier-flowering superior spikelets (SS). However, the links between the abundance of transcripts and their corresponding proteins are unclear. In this study, a SWATH-MS (sequential window acquisition of all theoretical spectra-mass spectrometry) -based quantitative proteomic analysis has been applied between SS and IS. A total of 304 proteins, ranging from cellular components to biological processes, were observed to be differentially expressed between IS and SS. Detailed gene ontology analysis indicated that several biological processes including photosynthesis, protein metabolism, and energy metabolism are differentially regulated. Further correlation analysis revealed that abundance of most of the differentially expressed proteins is not correlated to the transcript levels, indicating an extra layer of gene regulation which may exist during rice grain filling. These findings raise an intriguing possibility that these candidate proteins may be crucial in determining the poor grain-filling of IS. Therefore, we hypothesize that the regulation of proteome changes not only occurs at the transcriptional, but also at the post-transcriptional level, during grain filling in rice.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:34:24.486.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fuyuan Zhu
SpeciesList	scientific name: Oryza sativa (Rice); NCBI TaxID: 4530;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2016-11-21 03:52:52	ID requested
1	2017-07-03 01:28:44	announced
⏵ 2	2024-10-22 04:34:32	announced	2024-10-22: Updated project metadata.

Zhu FY, Chen MX, Su YW, Xu X, Ye NH, Cao YY, Lin S, Liu TY, Li HX, Wang GQ, Jin Y, Gu YH, Chan WL, Lo C, Peng X, Zhu G, Zhang J, SWATH-MS Quantitative Analysis of Proteins in the Rice Inferior and Superior Spikelets during Grain Filling. Front Plant Sci, 7():1926(2016) [pubmed]

10.3389/fpls.2016.01926;

curator keyword: Biological

submitter keyword: proteomics,SWATH-MS analysis, grain filling, rice., post-transcriptional regulation

Zhang Jianhua
contact affiliation	The Chinese University of Hong Kong
contact email	jhzhang@cuhk.edu.hk
lab head
Fuyuan Zhu
contact affiliation	The university of HongKong
contact email	376392305@qq.com
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/2017/07/PXD005401

PRIDE project URI

• PRIDE
  1. PXD005401
     1. Label: PRIDE project
     2. Name: SWATH-MS quantitative analysis of proteins in the rice inferior and superior spikelets during grain filling