title: Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.
abstract: BACKGROUND
  Defining the location of genes and the precise nature of gene products remains a fundamental challenge in genome annotation. Interrogating tandem mass spectrometry data using genomic sequence provides an unbiased method to identify novel translation products. A six-frame translation of the entire human genome was used as the query database to search for novel blood proteins in the data from the Human Proteome Organization Plasma Proteome Project. Because this target database is orders of magnitude larger than the databases traditionally employed in tandem mass spectra analysis, careful attention to significance testing is required. Confidence of identification is assessed using our previously described Poisson statistic, which estimates the significance of multi-peptide identifications incorporating the length of the matching sequence, number of spectra searched and size of the target sequence database.
  
  
  RESULTS
  Applying a false discovery rate threshold of 0.05, we identified 282 significant open reading frames, each containing two or more peptide matches. There were 627 novel peptides associated with these open reading frames that mapped to a unique genomic coordinate placed within the start/stop points of previously annotated genes. These peptides matched 1,110 distinct tandem MS spectra. Peptides fell into four categories based upon where their genomic coordinates placed them relative to annotated exons within the parent gene.
  
  
  CONCLUSIONS
  This work provides evidence for novel alternative splice variants in many previously annotated genes. These findings suggest that annotation of the genome is not yet complete and that proteomics has the potential to further add to our understanding of gene structures.
authors.affiliation: Bioinformatics Program, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Damian
authors.initials: D
authors.lastname: Fermin
authors.forename: Baxter B
authors.initials: BB
authors.lastname: Allen
authors.forename: Thomas W
authors.initials: TW
authors.lastname: Blackwell
authors.forename: Rajasree
authors.initials: R
authors.lastname: Menon
authors.forename: Marcin
authors.initials: M
authors.lastname: Adamski
authors.forename: Yin
authors.initials: Y
authors.lastname: Xu
authors.forename: Peter
authors.initials: P
authors.lastname: Ulintz
authors.forename: Gilbert S
authors.initials: GS
authors.lastname: Omenn
authors.forename: David J
authors.initials: DJ
authors.lastname: States
mesh_terms: D017398:Alternative Splicing; D001798:Blood Proteins / Q000235:genetics; D030562:Databases, Protein; D020224:Expressed Sequence Tags; D005796:Genes; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D008957:Models, Genetic; D016366:Open Reading Frames; D010455:Peptides / Q000097:blood / Q000235:genetics*; D016012:Poisson Distribution; D011506:Proteins / Q000235:genetics; D040901:Proteomics / Q000379:methods*
chemical_list: D001798:Blood Proteins; D010455:Peptides; D011506:Proteins