Shotgun proteomics in neuroscience

Neuron. 2009 Jul 16;63(1):12-26. doi: 10.1016/j.neuron.2009.06.011.


Mass spectrometry-based proteomics is increasingly used to address basic and clinical questions in biomedical research through studies of differential protein expression, protein-protein interactions, and posttranslational modifications. The complex structural and functional organization of the human brain warrants the application of high-throughput, systematic approaches to understand the functional alterations under normal physiological conditions and the perturbations of neurological diseases. This primer focuses on shotgun-proteomics-based tandem mass spectrometry for the identification of proteins in a complex mixture. It describes the basic concepts of protein differential expression analysis and posttranslational modification analysis and discusses several strategies to improve the coverage of the proteome.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Brain / metabolism*
  • Databases, Protein
  • Humans
  • Mass Spectrometry / methods
  • Neurosciences / methods*
  • Protein Interaction Mapping
  • Proteome / genetics
  • Proteome / metabolism*
  • Proteomics / methods*


  • Proteome