Dataset Information

Comprehensive Proteomics Profiling of Zebrafish Retina Using a Hybrid DDA/DIA-PASEF Spectral Library on a timsTOF Pro 2 Mass Spectrometer

ABSTRACT: 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.

INSTRUMENT(S):

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

TISSUE(S): Retina

DISEASE(S): Myopia

SUBMITTER: Chuen Lam

LAB HEAD: Prof. Thomas Lam

PROVIDER: PXD076440 | Pride | 2026-06-17

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	20251120_SW1_BB2_1_31426.d.zip	Other
	DDA_PASEF_raw_data.zip	Other
	DIA-NN_libBased_report.tsv	Tabular
	DIA-NN_libfree_report.csv	Csv
	DIA-NN_libfree_report.pg_matrix.tsv	Tabular

Items per page:

1 - 5 of 19

Similar Datasets

Project description:A quadrupole time-of-flight mass spectrometry coupled with a trapped ion mobility mass spectrometer operated in parallel accumulation-serial fragmentation mode has recently emerged as proteome profiling platform capable of providing four dimensional features of elution time, collision cross section, precursor and fragment ion masses of peptides. The PASEF mode has demonstrated its superior performance by providing nearly 100% ion sampling efficiency both in data-dependent acquisition and data-independent acquisition modes without sacrificing sensitivity. In addition, the substantial gain in selectivity has been proven in targeted measurements using PASEF integrated parallel reaction monitoring mode. However, because these are emerging technologies in the field of proteomics, their applicability to clinical samples has been less investigated. Cerebrospinal fluid is in direct contact with brain and has been shown to contain biomarkers related to a variety of neurological diseases although the proteomics data have been mainly generated using orbitrap-based mass spectrometers. Thus, we acquired in-depth proteome profiles of human CSF in DDA mode to generate a spectral library of 3,478 proteins. The benefit of applying the spectral library to PRM experiments was demonstrated by using CSF samples from 15 Alzheimer’s disease patients and 19 controls and utilizing the spectral library to determine elution times and ion mobility values of targeting peptide. Further, we acquired DIA data from the same CSF samples, and analyzed using the spectral library without additional efforts to generate study-specific library, which also resulted in sensitive protein identification compared to a library-free approach. Overall, we established resource of CSF proteome profiles with 4D features and demonstrated the significant gain for designing and analyzing targeted and DIA studies, which is expected to facilitate 4D proteomics of CSF to study various neurological disorders.

Dataset Information

Comprehensive Proteomics Profiling of Zebrafish Retina Using a Hybrid DDA/DIA-PASEF Spectral Library on a timsTOF Pro 2 Mass Spectrometer

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets