AI Article Synopsis
- Proteogenomics has uncovered previously unannotated open reading frames (ORFs) in mRNAs and noncoding RNAs, providing insights into their functional proteins.
- OpenProt annotates ORFs of at least 30 codons across various species, categorizing proteins into reference proteins (previously annotated) and noncanonical proteins, which include novel isoforms and entirely new proteins.
- The chapter also explains how to identify multiple ORFs within genes or transcripts and leverage OpenProt databases to find alternative proteins and novel isoforms using mass spectrometry-based proteomics.
Article Abstract
Proteogenomics has revealed the translation of unannotated open reading frames (ORFs) present in mRNAs and in noncoding RNAs (ncRNAs). OpenProt annotates all ORFs with a minimum of 30 codons in the transcriptome of several species and displays many functional features associated with the corresponding proteins. Two types of proteins are annotated: reference or canonical proteins which are proteins already annotated in UniProt, RefSeq, or Ensembl and noncanonical proteins. Noncanonical proteins form two groups: predicted novel isoforms that display a significant level of homology with a reference protein and alternative proteins that are new proteins with no significant homology to known proteins. This chapter describes how to check whether a gene and/or transcript contains multiple open reading frames and how to use OpenProt databases for the detection of alternative proteins and novel isoforms by mass spectrometry-based proteomics.
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| http://dx.doi.org/10.1007/978-1-0716-4007-4_1 | DOI Listing |
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