Diving into the Dark World of Ghost Proteins: Unraveling Their Functions

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Recent proteogenomic advances have expanded our understanding of the "Dark Proteome," which encompasses the full range of proteoforms, including post-translational modifications, isoforms, and alternative splicing variants. Within this framework, the "Ghost Proteome" specifically refers to non-canonical proteins absent from standard reference databases due to their unconventional origins. These alternative proteins (AltProts) arise from regions previously annotated as non-coding, such as untranslated regions (UTRs), alternative reading frames, and non-coding RNAs (ncRNAs, lncRNAs, circRNAs). Because AltProts lack molecular tools for characterization, their detection and functional annotation remain major challenges.
To address this, we are developing innovative strategies leveraging crosslinking mass spectrometry (XL-MS) to map AltProt interactions within cellular networks. This approach has already revealed AltProts interacting with known proteins, suggesting their involvement in key biological processes. Additionally, we have optimized crosslinked peptide detection through subcellular fractionation, leading to the identification of AltProts interacting with HLA-B at the B2M binding site, suggesting potential roles in MHC I complex stability or regulation.
By systematically integrating AltProts into protein interaction networks, we aim to uncover their contributions to cellular functions, shedding light on an overlooked layer of protein diversity

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