ArticlePloS one2010
An integrated mass-spectrometry pipeline identifies novel protein coding-regions in the human genome.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 30 citations in OpenAlex.
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- Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation.Annual review of analytical chemistry (Palo Alto, Calif.) · 2016Review
- Integrating genomic, transcriptomic, and interactome data to improve Peptide and protein identification in shotgun proteomics.Journal of proteome research · 2014Review
- A global non-coding RNA system modulates fission yeast protein levels in response to stress.Nature communications · 2014Article
- On the extent and role of the small proteome in the parasitic eukaryote Trypanosoma brucei.BMC biology · 2014Article
- HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.Nature methods · 2014Article
- The bacterial proteogenomic pipeline.BMC genomics · 2014Article
- Deducing protein function by forensic integrative cell biology.PLoS biology · 2013Article
- Deep coverage of the Escherichia coli proteome enables the assessment of false discovery rates in simple proteogenomic experiments.Molecular & cellular proteomics : MCP · 2013Article
- Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq.Molecular & cellular proteomics : MCP · 2013Article
- Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions.BMC genomics · 2013Article
- Inference and validation of protein identifications.Molecular & cellular proteomics : MCP · 2012Review
- Article
- The discovery of novel protein-coding features in mouse genome based on mass spectrometry data.Genomics · 2011Article
- OryzaPG-DB: rice proteome database based on shotgun proteogenomics.BMC plant biology · 2011Article
- Augmented annotation of the Schizosaccharomyces pombe genome reveals additional genes required for growth and viability.Genetics · 2011Article
- Proteomics of industrial fungi: trends and insights for biotechnology.Applied microbiology and biotechnology · 2011Review
- Functional genomic and proteomic analysis reveals disruption of myelin-related genes and translation in a mouse model of early life neglect.Frontiers in psychiatry · 2011Article
- A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics.Journal of proteomics · 2010Review
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundMost protein mass spectrometry (MS) experiments rely on searches against a database of known or predicted proteins, limiting their ability as a gene discovery tool.
resultsUsing 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.
conclusionsMS 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.
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