NDLI: Mass spectrometry at the interface of proteomics and genomics

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Back cover

Molecular BioSystems Vol -6

Molecular BioSystems Vol -5

Molecular BioSystems Vol -4

Molecular BioSystems Vol -3

Molecular BioSystems Vol -2

Mass spectrometry at the interface of proteomics and genomics

Content Provider	Royal Society of Chemistry (RSC)
Author	Krug, Karsten Nahnsen, Sven Macek, Boris
Copyright Year	2011
Abstract	With the onset of modern DNA sequencing technologies, genomics is experiencing a revolution in terms of quantity and quality of sequencing data. Rapidly growing numbers of sequenced genomes and metagenomes present a tremendous challenge for bioinformatics tools that predict protein-coding regions. Experimental evidence of expressed genomic regions, both at the RNA and protein level, is becoming invaluable for genome annotation and training of gene prediction algorithms. Evidence of gene expression at the protein level using mass spectrometry-based proteomics is increasingly used in refinement of raw genome sequencing data. In a typical “proteogenomics” experiment, the whole proteome of an organism is extracted, digested into peptides and measured by a mass spectrometer. The peptide fragmentation spectra are identified by searching against a six-frame translation of the raw genomic assembly, thus enabling the identification of hitherto unpredicted protein-coding genomic regions. Application of mass spectrometry to genome annotation presents a range of challenges to the standard workflows in proteomics, especially in terms of proteome coverage and database search strategies. Here we provide an overview of the field and argue that the latest mass spectrometry technologies that enable high mass accuracy at high acquisition rates will prove to be especially well suited for proteogenomics applications.
Starting Page	284
Ending Page	291
Page Count	8
File Format	HTM / HTML PDF
ISSN	1742206X
Volume Number	7
Issue Number	2
Journal	Molecular BioSystems
DOI	10.1039/c0mb00168f
Language	English
Publisher	Royal Society of Chemistry
Access Restriction	Open
Subject Keyword	Protein primary structure RNA Genomics Proteomics Proteome Genome Bioinformatics Mass spectrometry Protein DNA annotation DNA sequencing
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biotechnology

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