Identification of Small Open Reading Frame-Encoded Peptides in Glioma by an Optimized Proteomics Strategy

Small open reading frame-encoded peptides (SEPs), translated from previously unannotated genomic regions, have emerged as important regulators in diverse physiological and pathological processes. While ribosome profiling and bioinformatics analysis can predict putative SEPs, mass spectrometry (MS) is the only method for their definitive identification. However, MS-based SEP detection faces significant challenges due to SEP's short length and low abundance. To address these limitations, we developed an ammonium formate-mediated C8 solid-phase enrichment (AmF-C8-SPE) strategy that significantly outperforms classic C8-SPE, yielding superior SEP identification with enhanced unique peptide ratios and sequence coverage. By coupling AmF-C8-SPE with fractionation and LC-MS/MS analysis of glioma samples from 18 patients, we identified 549 novel SEPs, 113 of which exhibited differential expression between tumors and adjacent normal tissues. Importantly, randomly selected SEPs were validated by MS spectral matching with synthetic peptides and by confirming recombinant fusion protein expression in cells. Furthermore, Mfuzz clustering and ROC curve analyses revealed SEPs associated with glioma progression. DeepLoc-based prediction followed by confocal microscopy imaging confirmed nuclear localization of two candidate SEPs (IP_613981 and SPROHSA206836). Therefore, this study establishes an optimized SEP identification approach and the first comprehensive SEP profiling in glioma, providing a valuable resource to discover novel glioma biomarker and therapeutic target.