An integrated mass-spectrometry pipeline identifies novel protein coding-regions in the human genome.
Bitton, Danny A Smith, Duncan L Connolly, Yvonne Scutt, Paul J Miller, Crispin J
Bitton, Danny A
Smith, Duncan L
Connolly, Yvonne
Scutt, Paul J
Miller, Crispin J
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Abstract
BACKGROUND: Most protein mass spectrometry (MS) experiments rely on searches against a database of known or predicted proteins, limiting their ability as a gene discovery tool. RESULTS: Using a search against an in silico translation of the entire human genome, combined with a series of annotation filters, we identified 346 putative novel peptides [False Discovery Rate (FDR)<5%] in a MS dataset derived from two human breast epithelial cell lines. A subset of these were then successfully validated by a different MS technique. Two of these correspond to novel isoforms of Heterogeneous Ribonuclear Proteins, while the rest correspond to novel loci. CONCLUSIONS: MS technology can be used for ab initio gene discovery in human data, which, since it is based on different underlying assumptions, identifies protein-coding genes not found by other techniques. As MS technology continues to evolve, such approaches will become increasingly powerful.
Description
Date
2010
Publisher
Collections
Keywords
Tumour Cell Line
Type
Article
Citation
An integrated mass-spectrometry pipeline identifies novel protein coding-regions in the human genome. 2010, 5 (1):e8949 PLoS ONE