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

Raghothama Chaerkady, Dhanashree S. Kelkar, Babylakshmi Muthusamy, Kumaran Kandasamy, Sutopa B. Dwivedi, Nandini A. Sahasrabuddhe, Min Sik Kim, Santosh Renuse, Sneha M. Pinto, Rakesh Sharma, Harsh Pawar, Nirujogi Raja Sekhar, Ajeet Kumar Mohanty, Derese Getnet, Yi Yang, Jun Zhong, Aditya P. Dash, Robert M. MacCallum, Bernard Delanghe, Godfree MlamboAshwani Kumar, T. S.Keshava Prasad, Mobolaji Okulate, Nirbhay Kumar, Akhilesh Pandey

Research output: Contribution to journalArticle

44 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1872-1881
Number of pages10
JournalGenome Research
Volume21
Issue number11
DOIs
StatePublished - Nov 1 2011
Externally publishedYes

Fingerprint

Anopheles gambiae
Fourier Analysis
Mass Spectrometry
Genome
Genes
Untranslated Regions
Molecular Sequence Annotation
Peptides
Intergenic DNA
Proteomics
Introns
Malaria
Proteins
Complementary DNA
Proteogenomics
Databases
Ions
Technology
Polymerase Chain Reaction

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Chaerkady, R., Kelkar, D. S., Muthusamy, B., Kandasamy, K., Dwivedi, S. B., Sahasrabuddhe, N. A., ... Pandey, A. (2011). A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry. Genome Research, 21(11), 1872-1881. https://doi.org/10.1101/gr.127951.111

A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry. / Chaerkady, Raghothama; Kelkar, Dhanashree S.; Muthusamy, Babylakshmi; Kandasamy, Kumaran; Dwivedi, Sutopa B.; Sahasrabuddhe, Nandini A.; Kim, Min Sik; Renuse, Santosh; Pinto, Sneha M.; Sharma, Rakesh; Pawar, Harsh; Sekhar, Nirujogi Raja; Mohanty, Ajeet Kumar; Getnet, Derese; Yang, Yi; Zhong, Jun; Dash, Aditya P.; MacCallum, Robert M.; Delanghe, Bernard; Mlambo, Godfree; Kumar, Ashwani; Prasad, T. S.Keshava; Okulate, Mobolaji; Kumar, Nirbhay; Pandey, Akhilesh.

In: Genome Research, Vol. 21, No. 11, 01.11.2011, p. 1872-1881.

Research output: Contribution to journalArticle

Chaerkady, R, Kelkar, DS, Muthusamy, B, Kandasamy, K, Dwivedi, SB, Sahasrabuddhe, NA, Kim, MS, Renuse, S, Pinto, SM, Sharma, R, Pawar, H, Sekhar, NR, Mohanty, AK, Getnet, D, Yang, Y, Zhong, J, Dash, AP, MacCallum, RM, Delanghe, B, Mlambo, G, Kumar, A, Prasad, TSK, Okulate, M, Kumar, N & Pandey, A 2011, 'A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry', Genome Research, vol. 21, no. 11, pp. 1872-1881. https://doi.org/10.1101/gr.127951.111
Chaerkady R, Kelkar DS, Muthusamy B, Kandasamy K, Dwivedi SB, Sahasrabuddhe NA et al. A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry. Genome Research. 2011 Nov 1;21(11):1872-1881. https://doi.org/10.1101/gr.127951.111
Chaerkady, Raghothama ; Kelkar, Dhanashree S. ; Muthusamy, Babylakshmi ; Kandasamy, Kumaran ; Dwivedi, Sutopa B. ; Sahasrabuddhe, Nandini A. ; Kim, Min Sik ; Renuse, Santosh ; Pinto, Sneha M. ; Sharma, Rakesh ; Pawar, Harsh ; Sekhar, Nirujogi Raja ; Mohanty, Ajeet Kumar ; Getnet, Derese ; Yang, Yi ; Zhong, Jun ; Dash, Aditya P. ; MacCallum, Robert M. ; Delanghe, Bernard ; Mlambo, Godfree ; Kumar, Ashwani ; Prasad, T. S.Keshava ; Okulate, Mobolaji ; Kumar, Nirbhay ; Pandey, Akhilesh. / A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry. In: Genome Research. 2011 ; Vol. 21, No. 11. pp. 1872-1881.
@article{a063ebb611f9498d8d257c7bd8c08ba8,
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.",
author = "Raghothama Chaerkady and Kelkar, {Dhanashree S.} and Babylakshmi Muthusamy and Kumaran Kandasamy and Dwivedi, {Sutopa B.} and Sahasrabuddhe, {Nandini A.} and Kim, {Min Sik} and Santosh Renuse and Pinto, {Sneha M.} and Rakesh Sharma and Harsh Pawar and Sekhar, {Nirujogi Raja} and Mohanty, {Ajeet Kumar} and Derese Getnet and Yi Yang and Jun Zhong and Dash, {Aditya P.} and MacCallum, {Robert M.} and Bernard Delanghe and Godfree Mlambo and Ashwani Kumar and Prasad, {T. S.Keshava} and Mobolaji Okulate and Nirbhay Kumar and Akhilesh Pandey",
year = "2011",
month = "11",
day = "1",
doi = "10.1101/gr.127951.111",
language = "English (US)",
volume = "21",
pages = "1872--1881",
journal = "Genome Research",
issn = "1088-9051",
publisher = "Cold Spring Harbor Laboratory Press",
number = "11",

}

TY - JOUR

T1 - A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry

AU - Chaerkady, Raghothama

AU - Kelkar, Dhanashree S.

AU - Muthusamy, Babylakshmi

AU - Kandasamy, Kumaran

AU - Dwivedi, Sutopa B.

AU - Sahasrabuddhe, Nandini A.

AU - Kim, Min Sik

AU - Renuse, Santosh

AU - Pinto, Sneha M.

AU - Sharma, Rakesh

AU - Pawar, Harsh

AU - Sekhar, Nirujogi Raja

AU - Mohanty, Ajeet Kumar

AU - Getnet, Derese

AU - Yang, Yi

AU - Zhong, Jun

AU - Dash, Aditya P.

AU - MacCallum, Robert M.

AU - Delanghe, Bernard

AU - Mlambo, Godfree

AU - Kumar, Ashwani

AU - Prasad, T. S.Keshava

AU - Okulate, Mobolaji

AU - Kumar, Nirbhay

AU - Pandey, Akhilesh

PY - 2011/11/1

Y1 - 2011/11/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=80555142954&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=80555142954&partnerID=8YFLogxK

U2 - 10.1101/gr.127951.111

DO - 10.1101/gr.127951.111

M3 - Article

C2 - 21795387

AN - SCOPUS:80555142954

VL - 21

SP - 1872

EP - 1881

JO - Genome Research

JF - Genome Research

SN - 1088-9051

IS - 11

ER -