Discovery of Human sORF-Encoded Polypeptides (SEPs) in Cell Lines and Tissue

• Published in: Journal of proteome research Vol. 13; no. 3; pp. 1757 - 1765
• Main Authors: Ma, Jiao, Ward, Carl C, Jungreis, Irwin, Slavoff, Sarah A, Schwaid, Adam G, Neveu, John, Budnik, Bogdan A, Kellis, Manolis, Saghatelian, Alan
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 07.03.2014
• Subjects: Breast Neoplasms - chemistry; Breast Neoplasms - genetics; Cell Line; cell lines; Chromatography, Liquid; Codon, Initiator - chemistry; Codon, Initiator - genetics; Female; Genome, Human; Humans; K562 Cells; molecular biology; Open Reading Frames; Peptides - analysis; Peptides - chemistry; polypeptides; Protein Biosynthesis; proteome; Proteome - analysis; Proteome - chemistry; start codon; Tandem Mass Spectrometry; peptidomics; short open reading frames (sORFs); sORF-encoded peptides (SEPs)
• ISSN: 1535-3893; 1535-3907; 1535-3907
• DOI: 10.1021/pr401280w

The existence of nonannotated protein-coding human short open reading frames (sORFs) has been revealed through the direct detection of their sORF-encoded polypeptide (SEP) products. The discovery of novel SEPs increases the size of the genome and the proteome and provides insights into the molecular biology of mammalian cells, such as the prevalent usage of non-AUG start codons. Through modifications of the existing SEP-discovery workflow, we discover an additional 195 SEPs in K562 cells and extend this methodology to identify novel human SEPs in additional cell lines and human tissue for a final tally of 237 new SEPs. These results continue to expand the human genome and proteome and demonstrate that SEPs are a ubiquitous class of nonannotated polypeptides that require further investigation.