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.
摘要：
蛋白质基因组学已经揭示了存在于mRNA和非编码RNA(ncRNA)中的未注释开放阅读框(ORF)的翻译。OpenProt在几个物种的转录组中注释具有最少30个密码子的所有ORF，并显示与相应蛋白质相关的许多功能特征。注释了两种类型的蛋白质：参考或规范蛋白质，它们是在UniProt中已经注释的蛋白质，RefSeq,或Ensembl和非规范蛋白质。非规范蛋白质形成两组:预测的新同种型,其显示与参考蛋白质的显著水平的同源性,以及作为与已知蛋白质没有显著同源性的新蛋白质的替代蛋白质。本章介绍了如何检查基因和/或转录本是否包含多个开放阅读框，以及如何使用OpenProt数据库通过基于质谱的蛋白质组学检测替代蛋白质和新型同工型。
