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Large-scate database searching using tandem mass spectra: looking up the answer in the back of the book

Academic Article
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Overview

authors

  • Sadygov, R. G.
  • Cociorva, D.
  • Yates III, John

publication date

  • 2004

journal

  • Nature Methods  Journal

abstract

  • Database searching is an essential element of large-scale proteomics. Because these methods are widely used, it is important to understand the rationale of the algorithms. Most algorithms are based on concepts first developed in SEQUEST and PeptideSearch. Four basic approaches are used to determine a match between a spectrum and sequence: descriptive, interpretative, stochastic and probability-based matching. We review the basic concepts used by most search algorithms, the computational modeling of peptide identification and current challenges and limitations of this approach for protein identification.

subject areas

  • Algorithms
  • Amino Acid Sequence
  • Animals
  • Computer Simulation
  • Database Management Systems
  • Databases, Protein
  • Humans
  • Information Storage and Retrieval
  • Mass Spectrometry
  • Models, Chemical
  • Models, Statistical
  • Molecular Sequence Data
  • Proteins
  • Proteomics
  • Sequence Alignment
  • Sequence Analysis, Protein
  • User-Computer Interface
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Identity

International Standard Serial Number (ISSN)

  • 1548-7091

Digital Object Identifier (DOI)

  • 10.1038/nmeth725

PubMed ID

  • 15789030
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Additional Document Info

start page

  • 195

end page

  • 202

volume

  • 1

issue

  • 3

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