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
Chapter
Part of the Advances in Experimental Medicine and Biology book series (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.

Keywords

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 

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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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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