PXD068586

PXD068586 is an original dataset announced via ProteomeXchange.

Title	Impact of alternative splicing on Arabidopsis proteome (Part I, AspN)
Description	Alternative splicing (AS) is a key regulatory process in eukaryotes. Despite its importance, the impact of AS on proteome diversity in plants remains largely unexplored. Traditional tryptic digestion has limitations in detecting junction peptides because evolutionarily conserved nucleotide usage at exon boundaries increases the frequency of lysine- and arginine-coding triplets at exon ends, making detection of exon–exon and exon–intron junctions challenging. To address this gap, we performed a comprehensive analysis of the Arabidopsis proteome using the protease AspN combined with extensive offline fractionation. AspN is an endoprotease that cleaves at the N-terminal side of aspartic acid residues. To further enhance detection of alternatively spliced proteins, we analyzed both wild-type plants and the AS mutant acinus pinin. This approach enabled identification of isoform-specific peptides—both annotated and previously unannotated—using in-house algorithms and rigorous filtering steps. Our findings demonstrate that alternative splicing contributes substantially to proteome diversity in plants.
HostingRepository	PRIDE
AnnounceDate	2026-06-08
AnnouncementXML	Submission_2026-06-07_18:05:48.257.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Shouling Xu
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: NEWT:3702;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-09-19 10:59:36	ID requested
⏵ 1	2026-06-07 18:05:49	announced

10.1093/nar/gkag400;

Reyes AV, Zhang C, Karunadasa SS, Shrestha R, Grismer TS, Byun D, Xu SL, Impact of alternative splicing on Arabidopsis proteome. Nucleic Acids Res, 54(8):(2026) [pubmed]

submitter keyword: Tandem Mass Tags (TMT), ACINUS, AspN, protease, Proteome, Transcriptomics, Alternative Splicing

Shouling Xu
contact affiliation	Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA
contact email	sxu@carnegiescience.edu
lab head
Shouling Xu
contact affiliation	Carnegie Institution at Stanford
contact email	sxu@ciw.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/2026/06/PXD068586

PRIDE project URI

• PRIDE
  1. PXD068586
     1. Label: PRIDE project
     2. Name: Impact of alternative splicing on Arabidopsis proteome (Part I, AspN)