Gene model detection using mass spectrometry.

Bindu Nanduri; Nan Wang; Mark L. Lawrence; Susan M. Bridges; Shane C. Burgess

doi:10.1007/978-1-60761-444-9_10

Gene model detection using mass spectrometry.

Bindu Nanduri, Nan Wang, Mark L. Lawrence, Susan M. Bridges, Shane C. Burgess

Research output: Contribution to journal › Article › peer-review

5 Scopus citations

Abstract

The utility of a genome sequence in biological research depends entirely on the comprehensive description of all of its functional elements. Analysis of genome sequences is still predominantly gene-centric (i.e., identifying gene models/open reading frames). In this article, we describe a proteomics-based method for identifying open reading frames that are missed by computational algorithms. Mass spectrometry-based identification of peptides and proteins from biological samples provide evidence for the expression of the genome sequence at the protein level. This proteogenomic annotation method combines computationally predicted ORFs and the genome sequence with proteomics to identify novel gene models. We also describe our proteogenomic mapping pipeline - a set of computational tools that automate the proteogenomic annotation work flow. This pipeline is available for download at www.agbase.msstate.edu/tools/ .

Original language	English (US)
Pages (from-to)	137-144
Number of pages	8
Journal	Methods in molecular biology (Clifton, N.J.)
Volume	604
DOIs	https://doi.org/10.1007/978-1-60761-444-9_10
State	Published - 2010
Externally published	Yes

ASJC Scopus subject areas

Molecular Biology
Genetics

Access to Document

10.1007/978-1-60761-444-9_10

Cite this

@article{8a40da4236ab4a9a9157f3facc1c433f,

title = "Gene model detection using mass spectrometry.",

abstract = "The utility of a genome sequence in biological research depends entirely on the comprehensive description of all of its functional elements. Analysis of genome sequences is still predominantly gene-centric (i.e., identifying gene models/open reading frames). In this article, we describe a proteomics-based method for identifying open reading frames that are missed by computational algorithms. Mass spectrometry-based identification of peptides and proteins from biological samples provide evidence for the expression of the genome sequence at the protein level. This proteogenomic annotation method combines computationally predicted ORFs and the genome sequence with proteomics to identify novel gene models. We also describe our proteogenomic mapping pipeline - a set of computational tools that automate the proteogenomic annotation work flow. This pipeline is available for download at www.agbase.msstate.edu/tools/ .",

author = "Bindu Nanduri and Nan Wang and Lawrence, {Mark L.} and Bridges, {Susan M.} and Burgess, {Shane C.}",

year = "2010",

doi = "10.1007/978-1-60761-444-9_10",

language = "English (US)",

volume = "604",

pages = "137--144",

journal = "Methods in molecular biology (Clifton, N.J.)",

issn = "1064-3745",

publisher = "Humana Press Inc.",

}

TY - JOUR

T1 - Gene model detection using mass spectrometry.

AU - Nanduri, Bindu

AU - Wang, Nan

AU - Lawrence, Mark L.

AU - Bridges, Susan M.

AU - Burgess, Shane C.

PY - 2010

Y1 - 2010

N2 - The utility of a genome sequence in biological research depends entirely on the comprehensive description of all of its functional elements. Analysis of genome sequences is still predominantly gene-centric (i.e., identifying gene models/open reading frames). In this article, we describe a proteomics-based method for identifying open reading frames that are missed by computational algorithms. Mass spectrometry-based identification of peptides and proteins from biological samples provide evidence for the expression of the genome sequence at the protein level. This proteogenomic annotation method combines computationally predicted ORFs and the genome sequence with proteomics to identify novel gene models. We also describe our proteogenomic mapping pipeline - a set of computational tools that automate the proteogenomic annotation work flow. This pipeline is available for download at www.agbase.msstate.edu/tools/ .

AB - The utility of a genome sequence in biological research depends entirely on the comprehensive description of all of its functional elements. Analysis of genome sequences is still predominantly gene-centric (i.e., identifying gene models/open reading frames). In this article, we describe a proteomics-based method for identifying open reading frames that are missed by computational algorithms. Mass spectrometry-based identification of peptides and proteins from biological samples provide evidence for the expression of the genome sequence at the protein level. This proteogenomic annotation method combines computationally predicted ORFs and the genome sequence with proteomics to identify novel gene models. We also describe our proteogenomic mapping pipeline - a set of computational tools that automate the proteogenomic annotation work flow. This pipeline is available for download at www.agbase.msstate.edu/tools/ .

UR - http://www.scopus.com/inward/record.url?scp=77449141646&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77449141646&partnerID=8YFLogxK

U2 - 10.1007/978-1-60761-444-9_10

DO - 10.1007/978-1-60761-444-9_10

M3 - Article

C2 - 20013369

AN - SCOPUS:77449141646

SN - 1064-3745

VL - 604

SP - 137

EP - 144

JO - Methods in molecular biology (Clifton, N.J.)

JF - Methods in molecular biology (Clifton, N.J.)

ER -

Gene model detection using mass spectrometry.

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this