Mass Spectrometry-Based Proteomics: Basic Principles and Emerging Technologies and Directions

  • Susan K. Van Riper
  • Ebbing P. de Jong
  • John V. Carlis
  • Timothy J. Griffin
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 990)


As the main catalytic and structural molecules within living systems, proteins are the most likely biomolecules to be affected by radiation exposure. Proteomics, the comprehensive characterization of proteins within complex biological samples, is therefore a research approach ideally suited to assess the effects of radiation exposure on cells and tissues. For comprehensive characterization of proteomes, an analytical platform capable of quantifying protein abundance, identifying post-translation modifications and revealing members of protein complexes on a system-wide level is necessary. Mass spectrometry (MS), coupled with technologies for sample fractionation and automated data analysis, provides such a versatile and powerful platform. In this chapter we offer a view on the current state of MS-proteomics, and focus on emerging technologies within three areas: (1) New instrumental methods; (2) New computational methods for peptide identification; and (3) Label-free quantification. These emerging technologies should be valuable for researchers seeking to better understand biological effects of radiation on living systems.


Proteome Mass spectrometry Matrix-assisted laser desorption/ionization MALDI Electrospray ionization ESI Nanoscale reversed-phase liquid chromatography NanoLC Sequence database SEQUEST Mascot 2-dimensional gel electrophoresis Phosphorylation Glycosylation Isotope labeling Peptide sequencing Peptide identification 



Two-dimensional gel electrophoresis


Absolute protein expression




Collision activated dissociation


Collision induced dissociation


Electron capture dissociation


Electrospray ionization


Electron transfer dissociation


Field-assymetry ion mobility spectrometry


False discovery rate


High-energy collision dissociation


Human proteome organization


Isotope coded affinity tags


Ion mobility spectrometry


Infrared multiphoton dissociation


Isotope tagging for relative and absolute quantification


Liquid chromatography




Matrix-assisted laser desorption/ ionization


Multiple reaction monitoring


Mass spectrometry


Tandem mass spectrometry


National institute of standards and testing


Normalized spectral abundance factor


Protein abundance index


Pulsed Q dissociation


Post-translational modification


Stable isotope labeling of amino acids in cell culture


Selected reaction monitoring


Tandem mass tags


Correlation score


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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Susan K. Van Riper
    • 1
  • Ebbing P. de Jong
    • 2
  • John V. Carlis
    • 1
    • 3
  • Timothy J. Griffin
    • 1
    • 2
  1. 1.Department of Biomedical Informatics and Computational BiologyUniversity of MinnesotaMinneapolisUSA
  2. 2.Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisUSA
  3. 3.Department of Computer Science and EngineeringUniversity of MinnesotaMinneapolisUSA

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