PXD068593-1

PXD068593 is an original dataset announced via ProteomeXchange.

Title	Impact of alternative splicing on Arabidopsis proteome (Part III, TMT RT-SPS-MS3)
Description	Alternative splicing (AS) is a key regulatory process in eukaryotes. Despite its importance, the impact of AS on plant protein diversity and its global effect on the proteome remain largely unexplored. To address this, we included the AS acinus pinin mutant in our qualitative proteomic analysis to identify splice variants, and in our quantitative analysis to assess the impact of intron retention (IR) on protein abundance. Specifically, we (1) investigated global proteomic changes in acinus pinin double mutants using tandem mass tag (TMT) labeling. ACINUS and PININ are evolutionarily conserved splicing factors, and their disruption induces splicing events resembling those triggered by various stressors. We employed TMT labeling with real-time search MS3 (RTS-SPS-MS3), combined with extensive sample fractionation, to maximize proteome coverage and achieve accurate quantification. (2) To enhance isoform-specific peptide detection, we incorporated data generated using the alternative protease AspN, along with mined data from the Arabidopsis Proteome Draft (Mergner et al., 2020, Nature). This TMT-based approach allowed us to assess how increased intron retention (IIR) affects the proteome by integrating proteomic data with matched transcriptomic profiles. Moreover, our method enabled identification of isoform-specific peptides—both annotated and previously unannotated—using in-house algorithms and filtering steps. These findings demonstrate that alternatively spliced transcripts are translated and detectable at the protein level, providing insight into the functional consequences of isoform diversity and revealing the complex relationship between AS and protein abundance.
HostingRepository	PRIDE
AnnounceDate	2026-06-08
AnnouncementXML	Submission_2026-06-07_17:25:52.830.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 13:28:09	ID requested
⏵ 1	2026-06-07 17:25:53	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, 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/PXD068593

PRIDE project URI

• PRIDE
  1. PXD068593
     1. Label: PRIDE project
     2. Name: Impact of alternative splicing on Arabidopsis proteome (Part III, TMT RT-SPS-MS3)