Dataset Information

Time-resolved proteomic analysis in zebrafish larvae using bioorthogonal noncanonical amino acid tagging (BONCAT)

ABSTRACT: Protein synthesis underpins many biological processes, yet tracking time-dependent proteomic changes remains challenging. Bioorthogonal noncanonical amino acid tagging (BONCAT) offers a targeted approach for labeling and identifying newly synthesized proteins within defined time windows of interest. Here, we present the first such application of BONCAT in larval zebrafish, a model organism that has seen widespread use because of its genetic tractability and utility in developmental biology and neuroscience. We successfully enriched, using click chemistry, and identified, via mass spectrometry, azidohomoalanine (AHA)-labeled proteins after labeling durations as short as 12 hours. Proteomic analysis of BONCAT-enriched proteins demonstrated significant signal above background compared to unlabeled controls after both 48 h and 12 h of labeling. As a proof of concept, we investigated proteomic changes in response to heat shock in zebrafish larvae. BONCAT analysis revealed the upregulation of heat shock-induced proteins with greater sensitivity than whole lysate proteomics. Gene set enrichment analysis confirmed that known heat shock response proteins were significantly enriched in the BONCAT dataset but not in the whole lysate dataset, highlighting the ability of BONCAT to detect transient molecular responses otherwise masked in conventional whole lysate approaches. Beyond the expected changes in synthesis of heat shock proteins, BONCAT identified differentially expressed proteins implicated in stress responses, lipid metabolism, and neural regulation, offering insights into the zebrafish heat shock response. These findings establish BONCAT as a powerful tool for time-resolved proteomic analysis in zebrafish. Its ability to enhance signal specificity and resolve protein dynamics opens new avenues for studying molecular underpinnings of behavior, stress, and development in this versatile model organism.

INSTRUMENT(S):

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

TISSUE(S): Whole Body

SUBMITTER: Ting-Yu Wang

LAB HEAD: Tsui-Fen Chou

PROVIDER: PXD063084 | Pride | 2026-06-08

REPOSITORIES: Pride

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			Action	DRS
	Table_proteomics_related_to_fig2.xlsx	Xlsx
	Table_proteomics_related_to_fig3.xlsx	Xlsx
	Table_proteomics_related_to_fig4.xlsx	Xlsx
	Table_proteomics_related_to_fig5.xlsx	Xlsx
	fig2_0mM-1.raw	Raw

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Publications

Time-Resolved Proteomic Analysis in Zebrafish Using Bioorthogonal Noncanonical Amino Acid Tagging.

Miller Sophie E SE Wang Ting-Yu TY Quan Baiyi B Cammidge Tasha T Chou Tsui-Fen TF Prober David A DA Tirrell David A DA

Journal of proteome research 20260414 5

Tracking time-dependent proteomic changes remains challenging. Bioorthogonal noncanonical amino acid tagging (BONCAT) offers a targeted approach for identifying proteins synthesized within defined time windows. Here, we describe BONCAT proteomic analysis in larval zebrafish, a model organism widely used for its genetic tractability and utility in developmental biology and neuroscience. We enriched and identified azidohomoalanine-labeled proteins via mass spectrometry after labeling durations as ...[more]

PMID: 41980224

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