PXD066755

PXD066755 is an original dataset announced via ProteomeXchange.

Title	A mouse photoreceptor proteome resource
Description	To enrich mouse rod and cone photoreceptors for mass spectrometric analysis, we optimized our previously established trituration-based fluorescence-activated cell sorting (FACS) strategy (see Lux et al., 2024 for details; PMID: 38481472). For quantitative mass spectrometry, we utilized an ion mobility-enhanced version of a data-independent acquisition (DIA) workflow with alternating low and elevated energy (referred to as UDMSE). Label-free protein quantification of rod and cone photoreceptor in comparison with retina samples revealed an enrichment of photoreceptor-specific proteins. More importantly, established photoreceptor markers were significantly enriched in the respective photoreceptor samples, which confirms the quality and specificity of our proteome resource. Among the proteins highly enriched in the cone photoreceptor samples, we identified Mpp6/Pals2, a protein uncharacterized in photoreceptors so far, and established it as a novel pan-cone photoreceptor marker by immunocytochemistry. As an example of the use of our resource for the characterization of retina- and photoreceptor-specific protein isoforms, we assessed the expression of the two known isoforms of Mpp6/Pals2, the canonical Pals2β and the 14 aa shorter splice variant Pals2α. We confidently identified a tryptic peptide that only occurs upon splicing, indicating the expression of the non-canonical Pals2α in cone photoreceptors. In summary, our proteome resource provides comprehensive details on the protein (isoform) composition of mouse rod and cone photoreceptors, making it a valuable research tool for the study of retina biology and pathology.
HostingRepository	PRIDE
AnnounceDate	2025-12-09
AnnouncementXML	Submission_2025-12-08_16:52:14.763.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Olaf Jahn
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	No PTMs are included in the dataset
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2025-07-30 05:20:24	ID requested
⏵ 1	2025-12-08 16:52:15	announced

Dataset with its publication pending

submitter keyword: label-free protein quantification, mass spectrometry, FACS,Retina, rod photoreceptors, cone photoreceptors, Mpp6/Pals2

Prof. Dr. Olaf Jahn
contact affiliation	Neuroproteomics Group Department of Molecular Neurobiology Max Planck Institute for Multidisciplinary Sciences Hermann-Rein-Str. 3 37075 Goettingen Germany
contact email	jahn@mpinat.mpg.de
lab head
Olaf Jahn
contact affiliation	Neuroproteomics Group Department of Molecular Neurobiology Max Planck Institute for Multidisciplinary Sciences Hermann-Rein-Str. 3 37075 Goettingen, Germany
contact email	jahn@mpinat.mpg.de
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/2025/12/PXD066755

PRIDE project URI

• PRIDE
  1. PXD066755
     1. Label: PRIDE project
     2. Name: A mouse photoreceptor proteome resource