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PLoS One. 2010 Jan 28;5(1):e8949. doi: 10.1371/journal.pone.0008949.

An integrated mass-spectrometry pipeline identifies novel protein coding-regions in the human genome.

Author information

1
Applied Computational Biology and Bioinformatics Group, Cancer Research UK, Paterson Institute for Cancer Research, The University of Manchester, Manchester, United Kingdom.

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.

PMID:
20126623
PMCID:
PMC2812506
DOI:
10.1371/journal.pone.0008949
[Indexed for MEDLINE]
Free PMC Article
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