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A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry. 2011
Raghothama Chaerkady, and
Dhanashree S Kelkar, and
Babylakshmi Muthusamy, and
Kumaran Kandasamy, and
Sutopa B Dwivedi, and
Nandini A Sahasrabuddhe, and
Min-Sik Kim, and
Santosh Renuse, and
Sneha M Pinto, and
Rakesh Sharma, and
Harsh Pawar, and
Nirujogi Raja Sekhar, and
Ajeet Kumar Mohanty, and
Derese Getnet, and
Yi Yang, and
Jun Zhong, and
Aditya P Dash, and
Robert M MacCallum, and
Bernard Delanghe, and
Godfree Mlambo, and
Ashwani Kumar, and
T S Keshava Prasad, and
Mobolaji Okulate, and
Nirbhay Kumar, and
Akhilesh Pandey
McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland 21205, USA.
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.
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