PXD068589

PXD068589 is an original dataset announced via ProteomeXchange.

Title	Impact of alternative splicing on Arabidopsis proteome (Part II, TMT MS2, batch I)
Description	Alternative splicing (AS) is an important regulatory process in eukaryotes and, in plants, is influenced by various stressors and developmental stages. Despite its significance, the impact of AS on proteome diversity in plants has not been fully explored. To address this gap, we investigated isoform-specific peptides in wild-type (WT) plants and acinus pinin double mutants. ACINUS and PININ are evolutionarily conserved splicing factors, and their disruption induces splicing events resembling those triggered by diverse abiotic and biotic stressors. We generated extensively fractionated samples from a pooled peptide mix containing five replicates each of WT and acinus pinin, labeled with TMT11. This dataset was integrated with additional data generated using the alternative protease AspN, as well as mined data from the Arabidopsis Proteome Draft (Mergner et al., 2020, Nature), to enhance isoform-specific peptide detection. Using in-house algorithms and tailored filtering steps, this approach enabled identification of isoform-specific peptides, both annotated and previously unannotated. Our findings demonstrate that alternative splicing contributes substantially to proteome diversity in plants.
HostingRepository	PRIDE
AnnounceDate	2026-06-08
AnnouncementXML	Submission_2026-06-07_17:37:55.099.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	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2025-09-19 12:53:19	ID requested
⏵ 1	2026-06-07 17:37:55	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), Proteome, Transcriptomics, Alternative Splicing

Shouling Xu
contact affiliation	Department of Plant Biology, Carnegie Institution for Science, Stanford, California
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/PXD068589

PRIDE project URI

• PRIDE
  1. PXD068589
     1. Label: PRIDE project
     2. Name: Impact of alternative splicing on Arabidopsis proteome (Part II, TMT MS2, batch I)