title: A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry.
abstract: Anopheles gambiae is a major mosquito vector responsible for malaria transmission, whose genome sequence was reported in 2002. Genome annotation is a continuing effort, and many of the approximately 13,000 genes listed in VectorBase for Anopheles gambiae are predictions that have still not been validated by any other method. To identify protein-coding genes of An. gambiae based on its genomic sequence, we carried out a deep proteomic analysis using high-resolution Fourier transform mass spectrometry for both precursor and fragment ions. Based on peptide evidence, we were able to support or correct more than 6000 gene annotations including 80 novel gene structures and about 500 translational start sites. An additional validation by RT-PCR and cDNA sequencing was successfully performed for 105 selected genes. Our proteogenomic analysis led to the identification of 2682 genome search-specific peptides. Numerous cases of encoded proteins were documented in regions annotated as intergenic, introns, or untranslated regions. Using a database created to contain potential splice sites, we also identified 35 novel splice junctions. This is a first report to annotate the An. gambiae genome using high-accuracy mass spectrometry data as a complementary technology for genome annotation.
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland 21205, USA.
authors.forename: Raghothama
authors.initials: R
authors.lastname: Chaerkady
authors.forename: Dhanashree S
authors.initials: DS
authors.lastname: Kelkar
authors.forename: Babylakshmi
authors.initials: B
authors.lastname: Muthusamy
authors.forename: Kumaran
authors.initials: K
authors.lastname: Kandasamy
authors.forename: Sutopa B
authors.initials: SB
authors.lastname: Dwivedi
authors.forename: Nandini A
authors.initials: NA
authors.lastname: Sahasrabuddhe
authors.forename: Min-Sik
authors.initials: MS
authors.lastname: Kim
authors.forename: Santosh
authors.initials: S
authors.lastname: Renuse
authors.forename: Sneha M
authors.initials: SM
authors.lastname: Pinto
authors.forename: Rakesh
authors.initials: R
authors.lastname: Sharma
authors.forename: Harsh
authors.initials: H
authors.lastname: Pawar
authors.forename: Nirujogi Raja
authors.initials: NR
authors.lastname: Sekhar
authors.forename: Ajeet Kumar
authors.initials: AK
authors.lastname: Mohanty
authors.forename: Derese
authors.initials: D
authors.lastname: Getnet
authors.forename: Yi
authors.initials: Y
authors.lastname: Yang
authors.forename: Jun
authors.initials: J
authors.lastname: Zhong
authors.forename: Aditya P
authors.initials: AP
authors.lastname: Dash
authors.forename: Robert M
authors.initials: RM
authors.lastname: MacCallum
authors.forename: Bernard
authors.initials: B
authors.lastname: Delanghe
authors.forename: Godfree
authors.initials: G
authors.lastname: Mlambo
authors.forename: Ashwani
authors.initials: A
authors.lastname: Kumar
authors.forename: T S
authors.initials: TS
authors.lastname: Keshava Prasad
authors.forename: Mobolaji
authors.initials: M
authors.lastname: Okulate
authors.forename: Nirbhay
authors.initials: N
authors.lastname: Kumar
authors.forename: Akhilesh
authors.initials: A
authors.lastname: Pandey
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D000852:Anopheles / Q000235:genetics* / Q000378:metabolism*; D002874:Chromosome Mapping; D018387:Codon, Initiator; D005091:Exons; D017344:Genes, Insect; D023281:Genomics; D007438:Introns; D013058:Mass Spectrometry; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010455:Peptides / Q000235:genetics; D040901:Proteomics; D022821:RNA Splice Sites; D015203:Reproducibility of Results; D020506:Untranslated Regions / Q000235:genetics
chemical_list: D018387:Codon, Initiator; D010455:Peptides; D022821:RNA Splice Sites; D020506:Untranslated Regions