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Radiation Proteomics pp 1–35Cite as

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

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Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 990))

Abstract

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.

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Notes

  1. 1.

    The terms “fragmentation” and “dissociation” are used interchangeably in the field.

Abbreviations

2DGE:

Two-dimensional gel electrophoresis

APEX:

Absolute protein expression

AUC:

Area-under-curve

CAD:

Collision activated dissociation

CID:

Collision induced dissociation

ECD:

Electron capture dissociation

ESI:

Electrospray ionization

ETD:

Electron transfer dissociation

FAIMS:

Field-assymetry ion mobility spectrometry

FDR:

False discovery rate

HCD:

High-energy collision dissociation

HUPO:

Human proteome organization

ICAT:

Isotope coded affinity tags

IMS:

Ion mobility spectrometry

IRMPD:

Infrared multiphoton dissociation

iTRAQ:

Isotope tagging for relative and absolute quantification

LC:

Liquid chromatography

m/z:

Mass-to-charge

MALDI:

Matrix-assisted laser desorption/ ionization

MRM:

Multiple reaction monitoring

MS:

Mass spectrometry

MS2 :

Tandem mass spectrometry

NIST:

National institute of standards and testing

NSAF:

Normalized spectral abundance factor

PAI:

Protein abundance index

PQD:

Pulsed Q dissociation

PTM:

Post-translational modification

SILAC:

Stable isotope labeling of amino acids in cell culture

SRM:

Selected reaction monitoring

TMT:

Tandem mass tags

Xcorr:

Correlation score

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Authors and Affiliations

  1. Department of Biomedical Informatics and Computational Biology, University of Minnesota, 321 Church St SE/6-155 Jackson Hall, Minneapolis, MN, 55455, USA

    Susan K. Van Riper, John V. Carlis & Timothy J. Griffin

  2. Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church St SE/6-155 Jackson Hall, Minneapolis, MN, 55455, USA

    Ebbing P. de Jong & Timothy J. Griffin

  3. Department of Computer Science and Engineering, University of Minnesota, 321 Church St SE/6-155 Jackson Hall, Minneapolis, MN, 55455, USA

    John V. Carlis

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  1. Susan K. Van Riper
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  2. Ebbing P. de Jong
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  4. Timothy J. Griffin
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Correspondence to Susan K. Van Riper .

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  1. Radiation and Nuclear Safety Authority, STUK, Laippatie 4, Helsinki, 00880, Finland

    Dariusz Leszczynski

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Van Riper, S.K., de Jong, E.P., Carlis, J.V., Griffin, T.J. (2013). Mass Spectrometry-Based Proteomics: Basic Principles and Emerging Technologies and Directions. In: Leszczynski, D. (eds) Radiation Proteomics. Advances in Experimental Medicine and Biology, vol 990. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-5896-4_1

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