PXD063084-1

PXD063084 is an original dataset announced via ProteomeXchange.

Title	Time-resolved proteomic analysis in zebrafish larvae using bioorthogonal noncanonical amino acid tagging (BONCAT)
Description	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.
HostingRepository	PRIDE
AnnounceDate	2026-06-08
AnnouncementXML	Submission_2026-06-07_18:53:44.216.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ting-Yu Wang
SpeciesList	scientific name: Danio rerio (Zebrafish) (Brachydanio rerio); NCBI TaxID: NEWT:7955;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-17 18:20:20	ID requested
⏵ 1	2026-06-07 18:53:45	announced

Miller SE, Wang TY, Quan B, Cammidge T, Chou TF, Prober DA, Tirrell DA, Time-Resolved Proteomic Analysis in Zebrafish Using Bioorthogonal Noncanonical Amino Acid Tagging. J Proteome Res, 25(5):2263-2278(2026) [pubmed]

10.1021/acs.jproteome.5c00845;

submitter keyword: BONCAT, Heat Shock, Larval Zebrafish, Noncanonical Amino Acid Tagging, Protein Synthesis,Proteomics, Click Chemistry

Tsui-Fen Chou
contact affiliation	Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, United States
contact email	tfchou@caltech.edu
lab head
Ting-Yu Wang
contact affiliation	Caltech
contact email	tywang@caltech.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/PXD063084

PRIDE project URI

• PRIDE
  1. PXD063084
     1. Label: PRIDE project
     2. Name: Time-resolved proteomic analysis in zebrafish larvae using bioorthogonal noncanonical amino acid tagging (BONCAT)