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Anal Chem. 2016 Apr 5;88(7):3967-75. doi: 10.1021/acs.analchem.6b00191. Epub 2016 Mar 24.

Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides.

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Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States.
Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology , 10010 North Torrey Pines Road, La Jolla, California 92037, United States.
Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States.
MIT Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology , 32 Vassar Street, Cambridge, Massachusetts 02139, United States.
The Broad Institute of MIT and Harvard , 7 Cambridge Center, Cambridge, Massachusetts 02139, United States.


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.

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