Identification and analysis of short open reading frame-encoded peptides in different regions of mouse brain

Short open reading frame-encoded peptides (SEPs) are generally 2-100 amino acids in length and participate in various biological processes of the organism. The brain is the central hub of life activities, where different regions perform distinct functions. To characterize SEPs in brain regions, we analyzed SEPs in five mouse brain areas, including hippocampus, frontal cortex, temporal cortex, occipital cortex, and parietal cortex, with mass spectrometry-based proteomics. We obtained 1,095 proteins with less than 100 amino acids and identified 373 SEPs. Approximately 83% of these SEPs are reported for the first time. Half of them are encoded by ncRNA, and nearly one-third can find orthology across species. Specific SEPs were identified in each brain region. For example, IP_1018875 was identified in the frontal cortex, possibly related to autophagy and neuronal signaling. These results enrich the proteome of the mouse brain and help facilitate subsequent studies on the function of SEPs.