title: Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations.
abstract: We describe a general mass spectrometry-based approach for gene annotation of any organism and demonstrate its effectiveness using the nematode Caenorhabditis elegans. We detected 6779 C. elegans proteins (67,047 peptides), including 384 that, although annotated in WormBase WS150, lacked cDNA or other prior experimental support. We also identified 429 new coding sequences that were unannotated in WS150. Nearly half (192/429) of the new coding sequences were confirmed with RT-PCR data. Thirty-three (approximately 8%) of the new coding sequences had been predicted to be pseudogenes, 151 (approximately 35%) reveal apparent errors in gene models, and 245 (57%) appear to be novel genes. In addition, we verified 6010 exon-exon splice junctions within existing WormBase gene models. Our work confirms that mass spectrometry is a powerful experimental tool for annotating sequenced genomes. In addition, the collection of identified peptides should facilitate future proteomics experiments targeted at specific proteins of interest.
authors.affiliation: University of Washington, Department of Genome Sciences, Seattle, Washington 98195, USA.
authors.forename: Gennifer E
authors.initials: GE
authors.lastname: Merrihew
authors.forename: Colleen
authors.initials: C
authors.lastname: Davis
authors.forename: Brent
authors.initials: B
authors.lastname: Ewing
authors.forename: Gary
authors.initials: G
authors.lastname: Williams
authors.forename: Lukas
authors.initials: L
authors.lastname: Käll
authors.forename: Barbara E
authors.initials: BE
authors.lastname: Frewen
authors.forename: William Stafford
authors.initials: WS
authors.lastname: Noble
authors.forename: Phil
authors.initials: P
authors.lastname: Green
authors.forename: James H
authors.initials: JH
authors.lastname: Thomas
authors.forename: Michael J
authors.initials: MJ
authors.lastname: MacCoss
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000378:metabolism; D005091:Exons; D017238:Genes, Helminth; D049751:Genome, Helminth; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*
chemical_list: D020543:Proteome