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Stable Isotopic Labeling for Proteomics

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Sample Preparation in Biological Mass Spectrometry

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.

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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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Authors and Affiliations

  1. Centro Nacional de Investigaciones Oncológicas (CNIO), E-28029, Madrid, Spain

    Keith Ashman, María Isabel Ruppen Cañás & Fernando García Martínez

  2. Department Analytical Chemistry, University Complutense of Madrid, Av. Complutense s/n, E-28040, Madrid, Spain

    Jose L. Luque-Garcia

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  1. Keith Ashman
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  2. María Isabel Ruppen Cañás
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  3. Jose L. Luque-Garcia
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  4. Fernando García Martínez
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Correspondence to Keith Ashman .

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Editors and Affiliations

  1. , Department of Genetics and Complex Disea, Harvard School of Public Health, Harvard, Huntington Ave., SPH-1 665, Boston, 02115, Massachusetts, USA

    Alexander R. Ivanov

  2. , Research and Development, Pressure BioSciences, Inc., Norfolk Ave. 14, South Easton, 02375, Massachusetts, USA

    Alexander V. Lazarev

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Ashman, K., Cañás, M.I.R., Luque-Garcia, J.L., Martínez, F.G. (2011). Stable Isotopic Labeling for Proteomics. In: Ivanov, A., Lazarev, A. (eds) Sample Preparation in Biological Mass Spectrometry. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-0828-0_27

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