%0 Journal Article
%T Exploring the Alternative Proteome with OpenProt and Mass Spectrometry.
%A Provencher N
%A Leblanc S
%A Jacques JF
%A Roucou X
%J Methods Mol Biol
%V 2836
%N 0
%D 2024
%M 38995532
暂无%R 10.1007/978-1-0716-4007-4_1
%X 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.