What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome?

• DOI: 10.1016/j.mcpro.2023.100631
• Publication Date: 2023-08-11T01:41:39Z
• Authors: John R. Prensner; Jennifer G. Abelin; Leron W. Kok; Karl R. Clauser; Jonathan M. Mudge; Jorge Ruiz-Orera; Michal Bassani-St...; Robert L. Moritz; Eric W. Deutsch; Sebastiaan van He...
• Keywords: Proteome; RNA-Seq

Ribosome profiling (Ribo-Seq) has proven transformative for our understanding of the human genome and proteome by illuminating thousands noncanonical sites ribosome translation outside currently annotated coding sequences (CDSs). A conservative estimate suggests that at least 7000 ORFs are translated, which, first glance, potential to expand number protein CDSs 30%, from ∼19,500 over 26,000 CDSs. Yet, additional scrutiny these raised numerous questions about what fraction them truly produce a product those can be understood as proteins according conventional term. Adding further complication is fact published estimates vary widely around 30-fold, several thousand hundred thousand. The summation this research left genomics proteomics communities both excited prospect new regions in but searching guidance on how proceed. Here, we discuss current state ORF research, databases, interpretation, focusing assess whether given said "protein coding."