Proteomics

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Spatially-Resolved Top-Down Proteomics of Zebrafish Brain Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry

ABSTRACT: 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.

INSTRUMENT(S):

ORGANISM(S): Danio Rerio (zebrafish) (brachydanio Rerio)

TISSUE(S): Brain

SUBMITTER: Jorge Colon Rosado  

LAB HEAD: Liangliang Sun

PROVIDER: PXD070925 | Pride | 2026-06-08

REPOSITORIES: Pride

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Publications

Top-Down Proteomics of Zebrafish Brain Regions Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry.

Falamarzi Askarani Mehrdad M   Poulos William W   Rahimzadeh Dashtaki Maryam M   Fang Fei F   Cibelli Jose B JB   Sun Liangliang L  

Journal of proteome research 20260417 5

Understanding region-specific proteoform profiles in the brain is crucial for deciphering neural function and identifying therapeutic targets. Zebrafish (Danio rerio) is a valuable vertebrate model for neuroscience research due to its substantial conservation of brain structure and function with that of mammals. We present a label-free quantitative top-down proteomics (TDP) analysis of distinct zebrafish brain regions using microdissection and capillary zone electrophoresis-tandem mass spectrome  ...[more]

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