Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides.
Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides.
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DOI：
10.1021/acs.analchem.6b00191
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发表时间：
2016-04-05
影响因子：
7.4
通讯作者：
Saghatelian A
中科院分区：
文献类型：
--
作者：
Ma J;Diedrich JK;Jungreis I;Donaldson C;Vaughan J;Kellis M;Yates JR 3rd;Saghatelian A
计算、基因组学和蛋白质组学方法已被用于发现无注释的蛋白质编码小开放阅读框（smorf）。一些新的smorf在细胞和生物体中具有重要的生物学作用，这促使人们寻找更多的smorf。蛋白质组学的smORF发现方法是有优势的，因为它们检测smORF编码的多肽（SEP）来验证smORF的翻译和SEP的稳定性。由于SEP比一般蛋白质更短且含量更少，因此使用蛋白质组学进行SEP检测面临着独特的挑战。在这里，我们优化了SEP发现工作流程中的几个步骤，以提高SEP的隔离和识别。这些变化导致了几种新的人类SEP（新的人类基因）的检测，提高了对SEP分配的信心，并使SEP在不同细胞条件下的量化成为可能。这些改进将允许更快地检测和表征新的sep和smorf。
Computational, genomic, and proteomic approaches have been used to discover non-annotated protein-coding small open reading frames (smORFs). Some novel smORFs have crucial biological roles in cells and organisms, which motivates the search for additional smORFs. Proteomic smORF discovery methods are advantageous because they detect smORF-encoded polypeptides (SEPs) to validate smORF translation and SEP stability. Because SEPs are shorter and less abundant than average proteins, SEP detection using proteomics faces unique challenges. Here, we optimize several steps in the SEP discovery workflow to improve SEP isolation and identification. These changes have led to the detection of several new human SEPs (novel human genes), improved confidence in the SEP assignments, and enabled quantification of SEPs under different cellular conditions. These improvements will allow faster detection and characterization of new SEPs and smORFs.