PXD076440-1

PXD076440 is an original dataset announced via ProteomeXchange.

Title	Comprehensive Proteomics Profiling of Zebrafish Retina Using a Hybrid DDA/DIA-PASEF Spectral Library on a timsTOF Pro 2 Mass Spectrometer
Description	The zebrafish (Danio rerio) retina has been increasingly used for studying vertebrate visual processing and ocular growth regulation as it has a high anatomical and physiological similarity to the human eye. Recently, the integration of trapped ion mobility spectrometry (TIMS) with parallel accumulation–serial fragmentation (PASEF), has emerged as a powerful approach for proteomics analysis. In this study, a retina specific hybrid spectral library was constructed for quantitative proteomics analysis of the zebrafish retina. We integrated data dependent acquisition PASEF (DDA PASEF) and data independent acquisition PASEF (DIA PASEF) datasets acquired from 16 individual retinal protein lysates on a Bruker timsTOF Pro 2 mass spectrometer to generate the hybrid spectral library. The Pulsar search engine in Spectronaut 22 was used for hybrid library generation. The resulting hybrid library comprised 8,551 precursors, 7,866 unique peptides, and 1,494 protein groups (1% FDR), representing 44.5% of the reviewed zebrafish reference proteome.16 DIA PASEF runs from individual samples were then analyzed in both library based (using the hybrid library) and library free settings in Spectronaut (version 22) and DIA NN (version 2.3.2). It demonstrated that the hybrid library outperformed library free approaches, with improved peptide and precursor identifications across both proteomics platforms.
HostingRepository	PRIDE
AnnounceDate	2026-06-17
AnnouncementXML	Submission_2026-06-16_20:09:23.363.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chuen Lam
SpeciesList	scientific name: Danio rerio (Zebrafish) (Brachydanio rerio); NCBI TaxID: NEWT:7955;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2026-03-31 22:27:22	ID requested
⏵ 1	2026-06-16 20:09:23	announced
2	2026-06-20 21:17:37	announced	2026-06-21: Updated project metadata.

Dataset with its publication pending

submitter keyword: DIA,Retina, Zebrafish, DDA

Prof. Thomas Lam
contact affiliation	School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
contact email	thomas.c.lam@polyu.edu.hk
lab head
Chuen Lam
contact affiliation	The Hong Kong Polytechnic University/School of optometry
contact email	cclam@polyu.edu.hk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD076440
     1. Label: PRIDE project
     2. Name: Comprehensive Proteomics Profiling of Zebrafish Retina Using a Hybrid DDA/DIA-PASEF Spectral Library on a timsTOF Pro 2 Mass Spectrometer