TY  - JOUR
IS  - 1
N1  - © 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.
TI  - An Integrated Mass-Spectrometry Pipeline Identifies Novel Protein Coding-Regions in the Human Genome
AV  - public
VL  - 5
Y1  - 2010/01/28/
JF  - PLOS ONE
A1  - Bitton, DA
A1  - Smith, DL
A1  - Connolly, Y
A1  - Scutt, PJ
A1  - Miller, CJ
KW  - FALSE DISCOVERY RATES
KW  -  TILING ARRAYS
KW  -  GENE
KW  -  ANNOTATION
KW  -  SEARCH
KW  -  DATABASES
KW  -  PEPTIDES
KW  -  SEQUENCE
KW  -  MODEL
KW  -  PROTEOMICS
N2  - 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.
ID  - discovery1325266
PB  - PUBLIC LIBRARY SCIENCE
UR  - http://dx.doi.org/10.1371/journal.pone.0008949
SN  - 1932-6203
ER  -