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Shotgun protein identification and quantification by mass spectrometry in neuroproteomics

Academic Article
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Overview

authors

  • Lu, B.
  • Xu, T.
  • Park, S. K.
  • McClatchy, D. B.
  • Liao, L.
  • Yates III, John

publication date

  • 2009

journal

  • Methods in Molecular Biology  Journal

abstract

  • Shotgun proteomics is based on identification and quantification of peptides from digested proteins using tandem mass spectrometry. In this chapter, we discuss computational methods to analyze tandem mass spectra of peptides, including database searching, de novo peptide sequencing, hybrid approaches, library searching, and unrestricted modification search. A special focus is given to database searching programs, since they are the most widely used. The process of inferring proteins from identified peptides is then discussed. We also provide description of key steps in the quantitative analysis of mass spectrometry proteomics data. These methods are valuable tools for discovery and hypothesis-driven analyses in neuroproteomics.

subject areas

  • Amino Acid Sequence
  • Animals
  • Databases, Protein
  • Humans
  • Molecular Sequence Data
  • Nerve Tissue Proteins
  • Peptides
  • Proteomics
  • Tandem Mass Spectrometry
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Identity

International Standard Serial Number (ISSN)

  • 1064-3745 (Print) 1064-3745 (Linking)

Digital Object Identifier (DOI)

  • 10.1007/978-1-59745-562-6_16

PubMed ID

  • 20058176
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Additional Document Info

start page

  • 229

end page

  • 259

volume

  • 566

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