Shotgun proteomics: tools for the analysis of complex biological systems

Curr Opin Mol Ther. 2002 Jun;4(3):242-50.


Recent interest in proteomics has been fueled by the completion of multiple genome projects and ignited by the common need of biologists to rapidly and comprehensively evaluate complex samples of proteins on a global level. 'Shotgun proteomics' refers to the direct analysis of complex protein mixtures to rapidly generate a global profile of the protein complement within the mixture. This approach has been facilitated by the use of multidimensional protein identification technology (MudPIT), which incorporates multidimensional high-pressure liquid chromatography (LC/LC), tandem mass spectrometry (MS/MS) and database-searching algorithms. This review will focus on the most recent advances in methodologies for shotgun proteomics and address the limitations of the application of each to real biological samples.

Publication types

  • Research Support, U.S. Gov't, P.H.S.
  • Review

MeSH terms

  • Algorithms
  • Chromatography, High Pressure Liquid
  • Electrophoresis, Gel, Two-Dimensional
  • Mass Spectrometry
  • Membrane Proteins / analysis
  • Membrane Proteins / chemistry
  • Membrane Proteins / isolation & purification
  • Proteins / analysis
  • Proteins / chemistry
  • Proteins / genetics
  • Proteome / analysis*
  • Proteome / chemistry
  • Proteome / isolation & purification
  • Proteomics / instrumentation
  • Proteomics / methods*
  • Saccharomyces cerevisiae / chemistry
  • Software
  • Spectrometry, Mass, Electrospray Ionization
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization


  • Membrane Proteins
  • Proteins
  • Proteome