PXD022357

PXD022357 is an original dataset announced via ProteomeXchange.

Title	A co-fractionation mass spectrometry-based prediction of protein complex assemblies in the developing rice aleurone-subaleurone
Description	Multiprotein complexes execute and coordinate diverse cellular processes such as organelle biogenesis, vesicle trafficking, cell signaling, and metabolism. Knowledge about their composition and localization provides useful clues about the mechanisms of cellular homeostasis and systems-level control. This is of great biological importance and practical significance in heterotrophic rice (Oryza sativa) endosperm and aleurone-subaleurone tissues, which are a primary source of seed vitamins and stored energy. Dozens of protein complexes have been implicated in the synthesis, transport, and storage of seed proteins, lipids, vitamins, and minerals. Mutations in protein complexes that control RNA transport result in aberrant endosperm with shrunken and floury phenotypes, significantly reducing seed yield and quality. The purpose of this study was to broadly predict protein complex composition in the aleurone-subaleurone layers of developing rice seeds using co-fractionation mass spectrometry. Following orthogonal chromatographic separations of biological replicates, thousands of protein elution profiles were subjected to distance-based clustering to enable large-scale multimerization state measurements and protein complex predictions. The predicted complexes had predicted functions across diverse functional categories, including novel heteromeric RNA binding protein complexes that may influence seed quality. This effective and open-ended proteomics pipeline provides useful clues about systems-level post-translational control during the early stages of rice seed development.
HostingRepository	PRIDE
AnnounceDate	2022-02-17
AnnouncementXML	Submission_2022-02-17_05:41:07.581.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Youngwoo Lee
SpeciesList	scientific name: Oryza sativa (Rice); NCBI TaxID: 4530;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-04 08:26:52	ID requested
⏵ 1	2022-02-17 05:41:08	announced

Lee Y, Okita TW, Szymanski DB, A co-fractionation mass spectrometry-based prediction of protein complex assemblies in the developing rice aleurone-subaleurone. Plant Cell, 33(9):2965-2980(2021) [pubmed]

submitter keyword: rice, endosperm, aleurone, cytosolic, CF-MS, PCP, protein complex, prediction, composition

Daniel B. Szymanski
contact affiliation	Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907 Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907 Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
contact email	dszyman@purdue.edu
lab head
Youngwoo Lee
contact affiliation	Purdue University
contact email	lee1932@purdue.edu
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/2022/02/PXD022357

PRIDE project URI

• PRIDE
  1. PXD022357
     1. Label: PRIDE project
     2. Name: A co-fractionation mass spectrometry-based prediction of protein complex assemblies in the developing rice aleurone-subaleurone