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Stable Isotopic Labeling for Proteomics

  • Keith AshmanEmail author
  • María Isabel Ruppen Cañás
  • Jose L. Luque-Garcia
  • Fernando García Martínez
Chapter

Abstract

Since the coining of the term Proteome, the field of Proteomics has developed rapidly and come to rely heavily on mass spectrometry, initially for protein identification but recently the use of stable isotopic labels for protein quantitation has grown in importance. This trend has been driven by improvements in the mass spectrometers and reagents but also by the need to understand the molecular dynamics of cells. Since proteins are important effector molecules in most biochemical processes, key questions to be answered are: how much is present and when. In this chapter we describe the various methods currently available to quantitate proteins based on stable isotope protein labeling and discuss their merits as well as some of the issues still to be addressed.

Keywords

Proteomics Quantitation Stable isotope labeling iTRAQ SILAC Fractionation HPLC Mass spectrometer MALDI Electrospray Peptides Amines Protein Derivatization Biomarkers Metabolic Stoichiometry Chromatography 

Abbreviations

ACN

Acetonitrile

AQUA

Absolute quantification

CID

Collision induced disassociation

CILAT

Cleavable isobaric labeled affinity tag

ESI

Electrospray ionisation

iCAT

Isotopically coded affinity tags

iTRAQ

Isobaric tags for relative and absolute quantitation

HILIC

Hydrophilic interaction chromatography

HPLC

High performance liquid chromatography

ICPL

Isotope-coded protein label

ICPMS

Inductively coupled plasma mass spectrometry

IgG

Immunoglobulin

IPG

Immobilized pH gradient

IPG-IEF

Immobilized pH gradient isoelectric focusing

LC-MALDI MS/MS

Liquid chromatography matrix assisted laser desorption ionization tandem mass spectrometry

LC-MS

Liquid chromatography mass spectrometry

MALDI

Matrix assisted laser desorption ionisation

MMTS

Methyl methane-thiosulphonate

MS

Mass spectrometry

MS/MS

Tandem mass spectrometry

Nano RP LC

Nano reversed phase liquid chromatography

NHS

N-Hydroxysuccinamide

PBS

Phosphate buffered saline

QconCAT

Artificial proteins representing a quantification concatamer

qTOF MS/MS

Quadrupole time of flight tandem mass spectrometry

RP LC

Reversed phase liquid chromatography

SILAC

Stable isotope labeling by amino acids in cell culture

SCX

Strong cation exchange chromatography

SISCAPA

Stable isotope standards and capture by anti-peptide antibodies

TCA

Tri-chloroacetic acid

TCEP

Tris (2-carboxyethyl) phosphine

TEAB

Triethylammonium bicarbonate

TMT

Tandem Mass Tag Technology

TOF/TOF

Time of flight/time of flight

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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Keith Ashman
    • 1
    Email author
  • María Isabel Ruppen Cañás
    • 1
  • Jose L. Luque-Garcia
    • 2
  • Fernando García Martínez
    • 1
  1. 1.Centro Nacional de Investigaciones Oncológicas (CNIO)MadridSpain
  2. 2.Department Analytical ChemistryUniversity Complutense of MadridMadridSpain

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