PXD070925-1

PXD070925 is an original dataset announced via ProteomeXchange.

Title	Spatially-Resolved Top-Down Proteomics of Zebrafish Brain Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry
Description	Understanding region-specific proteoform profiles in the brain is crucial for deciphering neural function and identifying potential therapeutic targets. Here, we present a comprehensive label-free quantitative top-down proteomics (TDP) analysis of distinct zebrafish brain regions using capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS). We analyzed four anatomically distinct brain regions—telencephalon, combined habenula-optic tectum, cerebellum, and medulla isolated by manual dissection—identifying 1,746 proteoforms from 336 proteins. Only 89 proteoforms (5.1%) were shared across all brain regions, demonstrating substantial proteoform heterogeneity across the zebrafish brain. Quantitative analysis revealed region-specific expression patterns, with each comparison yielding 44-230 significantly differentially expressed proteoforms. Notably, six genes (SNCB, CALM1a, MBPA, PCP4L1, APOA2, and NEFMA) exhibited bidirectional proteoform regulation, with distinct proteoforms showing opposing regional expression patterns. Gene Ontology analysis revealed region-specific enrichment of biological processes: innate immune response and chromatin organization in cerebellum, actin filament organization in tectum/habenula, microtubule-based processes in telencephalon, and axonogenesis in medulla. Comparative analysis with bottom-up proteomics (BUP) revealed substantial discrepancies, with 10.8-31.8% of differentially expressed proteoforms undetected at the protein group level, highlighting the unique value of proteoform-specific characterization. This study establishes a comprehensive proteoform atlas of zebrafish brain regions and demonstrates the critical importance of TDP for understanding region-specific neural function through post-translational modification patterns invisible to conventional proteomics approaches.
HostingRepository	PRIDE
AnnounceDate	2026-06-08
AnnouncementXML	Submission_2026-06-07_16:37:41.968.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jorge Colon Rosado
SpeciesList	scientific name: Danio rerio (Zebrafish) (Brachydanio rerio); NCBI TaxID: NEWT:7955;
ModificationList	monomethylated residue; phosphorylated residue; acetylated residue; monohydroxylated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-11-18 19:15:42	ID requested
⏵ 1	2026-06-07 16:37:42	announced

10.1021/acs.jproteome.6c00007;

Falamarzi Askarani M, Poulos W, Rahimzadeh Dashtaki M, Fang F, Cibelli JB, Sun L, Top-Down Proteomics of Zebrafish Brain Regions Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry. J Proteome Res, 25(5):2546-2557(2026) [pubmed]

submitter keyword: ,proteoform,Top-down proteomics,Zebrafish brainregions

Liangliang Sun
contact affiliation	Department of Chemistry Michigan State University
contact email	lsun@chemistry.msu.edu
lab head
Jorge Colon Rosado
contact affiliation	Michigan State University
contact email	colonros@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/2026/06/PXD070925

PRIDE project URI

• PRIDE
  1. PXD070925
     1. Label: PRIDE project
     2. Name: Spatially-Resolved Top-Down Proteomics of Zebrafish Brain Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry