According to conventional assumptions, one eukaryotic mRNA carries a single annotated protein-coding sequence (CDS) and produces one protein only, and RNAs annotated as non-coding (ncRNAs and pseudogene RNAs) produce no proteins.
Within mRNAs, an alternative open reading frame (altORF) may be present in the UTRs in any of the three reading frames, or overlapping the annotated CDS in a frameshifted reading frame. RNAs annotated as non-coding may also carry potentially coding altORFs. Proteins translated from altORFs or alternative proteins (altProts) are not isoforms of currently annotated proteins; they are completely different.
Current conventions limit the size and complexity of the detectable proteome and prevent mass-spectrometry-based proteomics from providing a comprehensive characterization of biological systems. OpenProt enables improved mapping of the proteome because, in addition to currently annotated CDSs and proteins, OpenProt displays the sequence, functional annotation and expression evidence of previously hidden altORFs and their corresponding altProts. The OpenProt platform is freely available to users.