Tabea V. Riepe ¹ Merel Stemerdink ¹ Renee Salz ¹ Alfredo Dueñas Rey ² Suzanne E. De Bruijn ¹ Erica Boonen ¹ Tomasz Z. Tomkiewicz ¹ Michael Kwint ¹ Jolein Gloerich ¹ Hans J. Wessels ¹ Elfride De Baere ² Filip Van Nieuwerburgh ² Sarah De Keulenaer ² Barbara Ferrari ³ Stefano Ferrari ³ Frauke Coppieters ² Frans Cremers ¹ Erwin Van Wijk ¹ Susanne Roosing ¹ ERik De Vrieze ¹ Peter A. 't Hoen ^1*

• ¹ Radboud University Medical Centre, Nijmegen, Netherlands
• ² Ghent University, Ghent, East Flanders, Belgium
• ³ Fondazione Banca degli Occhi del Veneto Onlus - FBOV, Zelarino, Italy

The human neural retina is a complex tissue with abundant alternative splicing and more than 10% of genetic variants linked to inherited retinal diseases (IRDs) alter splicing. Traditional short-read RNAsequencing methods have been used for understanding retina-specific splicing but have limitations in detailing transcript isoforms. To address this, we generated a proteogenomic atlas that combines PacBio long-read RNA-sequencing data with mass spectrometry and whole genome sequencing data of three healthy human neural retina samples. We identified nearly 60,000 transcript isoforms, of which approximately one-third are novel. Additionally, ten novel peptides confirmed novel transcript isoforms. For instance, we identified a novel IMPDH1 isoform with a novel combination of known exons that is supported by peptide evidence. Our research underscores the potential of in-depth tissue-specific transcriptomic analysis to enhance our grasp of tissue-specific alternative splicing. The data underlying the proteogenomic atlas are available via EGA with identifier EGAD50000000101, via ProteomeXchange with identifier PXD045187, and accessible through the UCSC genome browser.