Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides

被引：107

作者：

Ma, Jiao ^{[1
,2
]}

Diedrich, Jolene K. ^{[2
,3
]}

Jungreis, Irwin ^{[4
,5
]}

Donaldson, Cynthia ^{[2
]}

Vaughan, Joan ^{[2
]}

Kellis, Manolis ^{[4
,5
]}

Yates, John R., III ^{[2
,3
]}

Saghatelian, Alan ^{[2
]}

机构：

[1] Harvard Univ, Dept Chem & Chem Biol, 12 Oxford St, Cambridge, MA 02138 USA

[2] Salk Inst Biol Studies, Clayton Fdn Labs Peptide Biol, 10010 N Torrey Pines Rd, La Jolla, CA 92037 USA

[3] Scripps Res Inst, Dept Physiol Chem, 10550 North Torrey Pines Rd, La Jolla, CA 92037 USA

[4] MIT, Comp Sci & Artificial Intelligence Lab, 32 Vassar St, Cambridge, MA 02139 USA

[5] Broad Inst MIT & Harvard, 7 Cambridge Ctr, Cambridge, MA 02139 USA

来源：

ANALYTICAL CHEMISTRY | 2016年 / 88卷 / 07期

关键词：

SHOTGUN PROTEOMICS; PEPTIDE; APOPTOSIS; RNA; CORTICOTROPIN; MORPHOGENESIS; TRANSLATION; ACTIVATION; COMPLEXITY; GENOMICS;

D O I：

10.1021/acs.analchem.6b00191

中图分类号：

O65 [分析化学];

学科分类号：

070302 ; 081704 ;

摘要：

Computational, genomic, and proteomic approaches have been used to discover nonannotated 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.

引用

页码：3967 / 3975

页数：9

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