Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins.

Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Research Abstract Details 

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Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Abstract Text:

Nuno Bandeira,Karl R Clauser,Pavel A Pevzner,

Despite significant advances in the identification of known proteins, the analysis of unknown proteins by MS/MS still remains a challenging open problem. Although Klaus Biemann recognized the potential of MS/MS for sequencing of unknown proteins in the 1980s, low throughput Edman degradation followed by cloning still remains the main method to sequence unknown proteins. The automated interpretation of MS/MS spectra has been limited by a focus on individual spectra and has not capitalized on the information contained in spectra of overlapping peptides. Indeed the powerful shotgun DNA sequencing strategies have not been extended to automated protein sequencing. We demonstrate, for the first time, the feasibility of automated shotgun protein sequencing of protein mixtures by utilizing MS/MS spectra of overlapping and possibly modified peptides generated via multiple proteases of different specificities. We validate this approach by generating highly accurate de novo reconstructions of multiple regions of various proteins in western diamondback rattlesnake venom. We further argue that shotgun protein sequencing has the potential to overcome the limitations of current protein sequencing approaches and thus catalyze the otherwise impractical applications of proteomics methodologies in studies of unknown proteins.

Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Publishing Authors By Initials

N Bandeira,KR Clauser,PA Pevzner,

For similar investigative techniques: chemistry, analytical: mass spectrometry: tandem mass spectrometry research abstracts see: investigative techniques: chemistry, analytical: mass spectrometry: tandem mass spectrometry research

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Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: Molecular & cellular proteomics : MCP

VOLUME: 6

Page Numbers: 1123-34

Journal Abbreviation: Mol. Cell Proteomics

ISSN: 1535-9476

DAY: 19

MONTH: 04

YEAR: 2007

Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Information

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LANGUAGE: eng

NlmUniqueID: 101125647

Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Keywords Mesh Terms:

KEYWORDS: Tandem Mass Spectrometry

MESH TERMS: methods

Chemical & Substance for Abstract: Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Information

Substance Name: Proteome

Registry Number: 0

Grant and Affiliation Information for Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins.

AFFILIATION: Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA. bandeira@cs.ucsd.edu

Country: United States

AGENCY: United States NCRR

GRANT: 1-R01-RR16522

ACRONYM: RR

MEDLINETA: Mol Cell Proteomics

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