Bitton, DA;
Smith, DL;
Connolly, Y;
Scutt, PJ;
Miller, CJ;
(2010)
An Integrated Mass-Spectrometry Pipeline Identifies Novel Protein Coding-Regions in the Human Genome.
PLOS ONE
, 5
(1)
, Article e8949. 10.1371/journal.pone.0008949.
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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.
| Type: | Article |
|---|---|
| Title: | An Integrated Mass-Spectrometry Pipeline Identifies Novel Protein Coding-Regions in the Human Genome |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1371/journal.pone.0008949 |
| Publisher version: | http://dx.doi.org/10.1371/journal.pone.0008949 |
| Language: | English |
| Additional information: | © 2010 Bitton et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. This project was funded by Cancer Research UK. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. |
| Keywords: | FALSE DISCOVERY RATES, TILING ARRAYS, GENE, ANNOTATION, SEARCH, DATABASES, PEPTIDES, SEQUENCE, MODEL, PROTEOMICS |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences |
| URI: | https://discovery.ucl.ac.uk/id/eprint/1325266 |
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