A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry

Genome Research

Volumn 21, Issue 11, 2011, Pages 1872-1881

  Chaerkady, Raghothama ^a,b   Kelkar, Dhanashree S ^b,c   Muthusamy, Babylakshmi ^b,d   Kandasamy, Kumaran ^a,b   Dwivedi, Sutopa B ^b,c   Sahasrabuddhe, Nandini A ^a,b,e   Kim, Min Sik ^a   Renuse, Santosh ^a,b,c   Pinto, Sneha M ^b,e   Sharma, Rakesh ^f   Pawar, Harsh ^b,g   Sekhar, Nirujogi Raja ^b,d   Mohanty, Ajeet Kumar ^h   Getnet, Derese ^a   Yang, Yi ^a   Zhong, Jun ^a   Dash, Aditya P ⁱ   MacCallum, Robert M ^j   Delanghe, Bernard ^k   Mlambo, Godfree ^l   Kumar, Ashwani ^h   Prasad, T S Keshava ^b,d,e   Okulate, Mobolaji ^m   Kumar, Nirbhay ^l,n   Pandey, Akhilesh ^a,o   more..

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Institute of Bioinformatics   (India)

^c AMRITA UNIVERSITY   (India)

^d PONDICHERRY UNIVERSITY   (India)

^e MANIPAL UNIVERSITY   (India)

^f NATIONAL INSTITUTE OF MENTAL HEALTH AND NEUROSCIENCES   (India)

^g RAJIV GANDHI UNIVERSITY OF HEALTH SCIENCES   (India)

^h National Institute of Malaria Research   (India)

ⁱ WORLD HEALTH ORGANIZATION   (Switzerland)

^j IMPERIAL COLLEGE LONDON   (United Kingdom)

^k THERMO FISHER SCIENTIFIC   (Germany)

^l JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^m UNIVERSITY OF MARYLAND EASTERN SHORE   (United States)

ⁿ TULANE UNIVERSITY   (United States)

^o JOHNS HOPKINS UNIVERSITY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; SPACER DNA;

ACCURACY; ANOPHELES GAMBIAE; ARTICLE; EXON; FOURIER TRANSFORM MASS SPECTROMETRY; GENE IDENTIFICATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC CODE; INSECT GENETICS; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEOMICS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA TRANSLATION; TRANSLATION INITIATION; UNINDEXED SEQUENCE; UTRICLE;

ALTERNATIVE SPLICING; ANIMALS; ANOPHELES GAMBIAE; CHROMOSOME MAPPING; CODON, INITIATOR; EXONS; GENES, INSECT; GENOMICS; INTRONS; MASS SPECTROMETRY; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PEPTIDES; PROTEOMICS; REPRODUCIBILITY OF RESULTS; RNA SPLICE SITES; UNTRANSLATED REGIONS;

ANOPHELES GAMBIAE;

EID: 80555142954     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.127951.111     Document Type: Article

References (33)

1. Baerenfaller K, Grossmann J, Grobei MA, Hull R, Hirsch-Hoffmann M, Yalovsky S, Zimmermann P, Grossniklaus U, Gruissem W, Baginsky S. 2008. Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 320: 938-941. (Pubitemid 351929590)
2. Birney E, Clamp M, Durbin R. 2004. GeneWise and Genomewise. Genome Res 14: 988-995. (Pubitemid 38660520)
3. Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S, Potthast F, Deutsch EW, Panse C, de Lichtenberg U, Rinner O, et al. 2007. A high-quality catalog of the Drosophila melanogaster proteome. Nat Biotechnol 25: 576-583. (Pubitemid 46834841)
4. Choudhary JS, Blackstock WP, Creasy DM, Cottrell JS. 2001. Matching peptide mass spectra to EST and genomic DNA databases. Trends Biotechnol 19: S17-S22.
5. Driessen HP, de Jong WW, Tesser GI, Bloemendal H. 1985. The mechanism of N-terminal acetylation of proteins. CRC Crit Rev Biochem 18: 281-325.
6. Eyras E, Caccamo M, Curwen V, Clamp M. 2004. ESTGenes: Alternative splicing from ESTs in Ensembl. Genome Res 14: 976-987. (Pubitemid 38660519)
7. Gevaert K, Goethals M, Martens L, Van Damme J, Staes A, Thomas GR, Vandekerckhove J. 2003. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat Biotechnol 21: 566-569. (Pubitemid 36532024)
8. Goetze S, Qeli E, Mosimann C, Staes A, Gerrits B, Roschitzki B, Mohanty S, Niederer EM, Laczko E, Timmerman E, et al. 2009. Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster. PLoS Biol 7: e1000236. doi: 10.1371/journal.pbio.1000236.
9. Gupta N, Benhamida J, Bhargava V, Goodman D, Kain E, Kerman I, Nguyen N, Ollikainen N, Rodriguez J, Wang J, et al. 2008. Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Res 18: 1133-1142. (Pubitemid 351931164)
10. Harsha HC, Molina H, Pandey A. 2008. Quantitative proteomics using stable isotope labeling with amino acids in cell culture. Nat Protoc 3: 505-516. (Pubitemid 351372235)
11. Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, et al. 2002. The genome sequence of the malaria mosquito Anopheles gambiae. Science 298: 129-149.
12. Kalume DE, Okulate M, Zhong J, Reddy R, Suresh S, Deshpande N, Kumar N, Pandey A. 2005a. A proteomic analysis of salivary glands of female Anopheles gambiae mosquito. Proteomics 5: 3765-3777. (Pubitemid 41393307)
13. Kalume DE, Peri S, Reddy R, Zhong J, Okulate M, Kumar N, Pandey A. 2005b. Genome annotation of Anopheles gambiae using mass spectrometry-derived data. BMC Genomics 6: 128. doi: 10.1186/1471-2164-6-128.
14. Korf I. 2004. Gene finding in novel genomes. BMC Bioinformatics 5: 59. doi: 10.1186/1471-2105-5-59.
15. Kuster B, Mortensen P, Andersen JS, Mann M. 2001. Mass spectrometry allows direct identification of proteins in large genomes. Proteomics 1: 641-650. (Pubitemid 33588315)
16. Lawson D, Arensburger P, Atkinson P, Besansky NJ, Bruggner RV, Butler R, Campbell KS, Christophides GK, Christley S, Dialynas E, et al. 2009. VectorBase: a data resource for invertebrate vector genomics. Nucleic Acids Res 37: D583-D587.
17. Li S, Ma L, Li H, Vang S, Hu Y, Bolund L, Wang J. 2007. Snap: an integrated SNP annotation platform. Nucleic Acids Res 35: D707-D710. (Pubitemid 46056296)
18. Mann M, Pandey A. 2001. Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases. Trends Biochem Sci 26: 54-61. (Pubitemid 32124711)
19. Menon R, Zhang Q, Zhang Y, Fermin D, Bardeesy N, DePinho RA, Lu C, Hanash SM, Omenn GS, States DJ. 2009. Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer. Cancer Res 69: 300-309.
20. Merrihew GE, Davis C, Ewing B, Williams G, Kall L, Frewen BE, Noble WS, Green P, Thomas JH, MacCoss MJ. 2008. Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Res 18: 1660-1669.
21. Molina H, Bunkenborg J, Reddy GH, Muthusamy B, Scheel PJ, Pandey A. 2005. A proteomic analysis of human hemodialysis fluid. Mol Cell Proteomics 4: 637-650. (Pubitemid 40862242)
22. Molina H, Horn DM, Tang N, Mathivanan S, Pandey A. 2007. Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci 104: 2199-2204. (Pubitemid 46391375)
23. Mongin E, Louis C, Holt RA, Birney E, Collins FH. 2004. The Anopheles gambiae genome: an update. Trends Parasitol 20: 49-52. (Pubitemid 38121256)
24. Okulate MA, Kalume DE, Reddy R, Kristiansen T, Bhattacharyya M, Chaerkady R, Pandey A, Kumar N. 2007. Identification and molecular characterization of a novel protein Saglin as a target of monoclonal antibodies affecting salivary gland infectivity of Plasmodium sporozoites. Insect Mol Biol 16: 711-722. (Pubitemid 350290889)
25. Oyama M, Kozuka-Hata H, Suzuki Y, Semba K, Yamamoto T, Sugano S. 2007. Diversity of translation start sites may define increased complexity of the human short ORFeome. Mol Cell Proteomics 6: 1000-1006.
26. Pandey A, Lewitter F. 1999. Nucleotide sequence databases: a gold mine for biologists. Trends Biochem Sci 24: 276-280. (Pubitemid 29301692)
27. Pandey A, Mann M. 2000. Proteomics to study genes and genomes. Nature 405: 837-846. (Pubitemid 30407862)
28. Peri S, Pandey A. 2001. A reassessment of the translation initiation codon in vertebrates. Trends Genet 17: 685-687. (Pubitemid 33097510)
29. Rozen S, Skaletsky H. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386.
30. Sevinsky JR, Cargile BJ, Bunger MK, Meng F, Yates NA, Hendrickson RC, Stephenson JL Jr. 2008. Whole genome searching with shotgun proteomic data: Applications for genome annotation. J Proteome Res 7: 80-88. (Pubitemid 351171118)
31. Suzuki Y, Sugano S. 2006. Transcriptome analyses of human genes and applications for proteome analyses. Curr Protein Pept Sci 7: 147-163.
32. Tress ML, Wesselink JJ, Frankish A, Lopez G, Goldman N, Loytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, et al. 2008. Determination and validation of principal gene products. Bioinformatics 24: 11-17.
33. Xia D, Sanderson SJ, Jones AR, Prieto JH, Yates JR, Bromley E, Tomley FM, Lal K, Sinden RE, Brunk BP, et al. 2008. The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation. Genome Biol 9: R116. doi: 10.1186/gb-2008-9-7-r116.