PXD059560

PXD059560 is an original dataset announced via ProteomeXchange.

Title	Data-independent acquisition parallel accumulation-serial fragmentation (diaPASEF) analysis of the separated zebrafish lens improves identifications
Description	Ocular lens fiber cells degrade their organelles during differentiation to prevent light scattering. Organelle degradation occurs continuously throughout an individual’s lifespan, creating a spatial gradient of young cortical fiber cells in the lens periphery to older nuclear fiber cells in the center of the lens. Therefore, separation of cortical and nuclear regions enables examination of protein aging. Previously, the human lens cortex and nucleus have been studied using data-independent acquisition (DIA) proteomics, allowing for the identification of low-abundance protein groups. In this study, we employed data-independent acquisition parallel accumulation-serial fragmentation (diaPASEF) proteomics to study the zebrafish lens proteome and compared results to a standard orbitrap DIA method. Using the additional ion mobility gas phase separation of diaPASEF, peptide and protein group identifications increased by over 200% relative to an orbitrap DIA method in the zebrafish lens. With diaPASEF, we identified 13,721 and 11,996 unique peptides in the zebrafish lens cortex and nucleus, which correspond to 1,537 and 1,389 protein groups. Thus, separation of the zebrafish lens into cortical and nuclear regions followed by diaPASEF analysis produced the most comprehensive zebrafish lens proteomic dataset to date.
HostingRepository	PRIDE
AnnounceDate	2025-03-20
AnnouncementXML	Submission_2025-03-20_12:50:45.480.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sarah Zelle
SpeciesList	scientific name: Danio rerio (Zebrafish) (Brachydanio rerio); NCBI TaxID: 7955;
ModificationList	L-methionine removal; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480; timsTOF HT

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-08 13:41:13	ID requested
⏵ 1	2025-03-20 12:50:45	announced

10.1101/2025.03.13.642445;

submitter keyword: DIA,Lens, diaPASEF, zebrafish, aging

Kevin Schey
contact affiliation	Department of Biochemistry, Vanderbilt University, USA
contact email	k.schey@vanderbilt.edu
lab head
Sarah Zelle
contact affiliation	Vanderbilt University
contact email	sarah.r.zelle@vanderbilt.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD059560
     1. Label: PRIDE project
     2. Name: Data-independent acquisition parallel accumulation-serial fragmentation (diaPASEF) analysis of the separated zebrafish lens improves identifications