PXD034368

PXD034368 is an original dataset announced via ProteomeXchange.

Title	Large-scale Top-down Proteomics of the Arabidopsis thaliana Leaf and Chloroplast Proteomes
Description	We present a large-scale top-down proteomics study of plant leaf and chloroplast proteins, achieving the identification of over 4700 unique proteoforms. Using capillary zone electrophoresis coupled with tandem mass spectrometry analysis of offline size-exclusion chromatography fractions, we identify 3198 proteoforms for total leaf and 1836 proteoforms for chloroplast, with 1024 and 363 proteoforms having post-translational modifications (PTMs), respectively. The electrophoretic mobility prediction of CZE allowed us to validate PTMs that impact the charge state such as acetylation and phosphorylation. Identified PTMs included Trp (di)oxidation events on six chloroplast proteins that may represent novel targets of singlet oxygen sensing. Furthermore, our top-down proteomics data provides direct experimental evidence of the N- and C-terminal residues of numerous mature proteoforms from chloroplast, mitochondria, endoplasmic reticulum, and other sub-cellular localizations. With this information, we propose transit peptide cleavage sites and correct sub-cellular localization signal predictions. This large-scale analysis illustrates the power of top-down proteoform identification of PTMs and intact sequences that can benefit our understanding of both the structure and function of hundreds of plant proteins.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_07:22:33.216.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Liangliang Sun
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	phosphorylated residue; acetylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-06 06:37:29	ID requested
1	2023-01-05 14:26:25	announced
⏵ 2	2023-11-14 07:22:34	announced	2023-11-14: Updated project metadata.

Wang Q, Sun L, Lundquist PK, Large-scale top-down proteomics of the Arabidopsis thaliana leaf and chloroplast proteomes. Proteomics, 23(3-4):e2100377(2023) [pubmed]

submitter keyword: Arabidopsis thaliana, post-translational modification, proteoform, transit peptide, singlet oxygen, chloroplast

Liangliang Sun
contact affiliation	Department of Chemistry, Michigan State University
contact email	lsun@chemistry.msu.edu
lab head
Liangliang Sun
contact affiliation	Michigan State University
contact email	lsun@chemistry.msu.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/2023/01/PXD034368

PRIDE project URI

• PRIDE
  1. PXD034368
     1. Label: PRIDE project
     2. Name: Large-scale Top-down Proteomics of the Arabidopsis thaliana Leaf and Chloroplast Proteomes